Volume Interactions Research Articles

A Backscatter Model Combing Wind and Rain Effect at Low Incidence Angles

As the Wind blows over the ocean surface, the generated waves are the primary factor affecting the microwave backscatter of the remote sensing radar. In addition, there are also some influencing factors, such as rainfall, which is the best-known atmospheric phenomenon. This paper proposes a wind and rain backscatter model whose angle of incidence is from 1 to 6 deg. The model is developed by considering the influence of ocean surface wind, atmospheric rain attenuation, rain volume backscatter and interactions between raindrops and ocean surface. The wind-induced component of the model adopted a quasi-specular theoretical model for the isotropic rough surface of Gaussian statistics. Rain attenuation is expressed as a coefficient of the model, and rain volume backscatter is expressed as a function of the rain volume backscattering coefficient, the thickness of precipitation layer and the incidence angle. Interactions between raindrops and ocean surface are complicated and deduced from the collocated dataset from the Precipitation Radar onboard the Tropical Rainfall Measuring Mission satellite and the European Centre for Medium-Range Weather Forecasts. Based on the collocated dataset, the result shows the proposed model can estimate reasonably accurate estimates surface backscatter within wind speeds range from 8 to 18 m s−1.

Self–dual solutions of a field theory model of two linked rings

In this work the connection established in [7,8] between a model of two linked polymers rings with fixed Gaussian linking number forming a 4-plat and the statistical mechanics of non-relativistic anyon particles is explored. The excluded volume interactions have been switched off and only the interactions of entropic origin arising from the topological constraints are considered. An interpretation from the polymer point of view of the field equations that minimize the energy of the model in the limit in which one of the spatial dimensions of the 4-plat becomes very large is provided. It is shown that the self-dual contributions are responsible for the long-range interactions that are necessary for preserving the global topological properties of the system during the thermal fluctuations. The non self-dual part is also related to the topological constraints, and takes into account the local interactions acting on the monomers in order to prevent the breaking of the polymer lines. It turns out that the energy landscape of the two linked rings is quite complex. Assuming as a rough approximation that the monomer densities of half of the 4-plat are constant, at least two points of energy minimum are found. Classes of non-trivial self-dual solutions of the self-dual field equations are derived. One of these classes is characterized by densities of monomers that are the squared modulus of holomorphic functions. The second class is obtained under some assumptions that allow to reduce the self-dual equations to an analog of the Gouy-Chapman equation for the charge distribution of ions in a double layer capacitor. In the present case, the spatial distribution of the electric potential of the ions is replaced by the spatial distribution of the fictitious magnetic fields associated with the presence of the topological constraints. In the limit in which two of the spatial dimensions are large in comparison with the third one, we provide exact formulas for the conformations of the monomer densities of the 4-plat by using the elliptic, hyperbolic and trigonometric solutions of the sinh-Gordon and cosh-Gordon equations which have been used for instance in the construction of classical string solutions in AdS3 and dS3 [9].

Microscopic interactions control a structural transition in active mixtures of microtubules and molecular motors

Microtubules and molecular motors are essential components of the cellular cytoskeleton, driving fundamental processes in vivo, including chromosome segregation and cargo transport. When reconstituted in vitro, these cytoskeletal proteins serve as energy-consuming building blocks to study the self-organization of active matter. Cytoskeletal active gels display rich emergent dynamics, including extensile flows, locally contractile asters, and bulk contraction. However, it is unclear how the protein-protein interaction kinetics set their contractile or extensile nature. Here, we explore the origin of the transition from extensile bundles to contractile asters in a minimal reconstituted system composed of stabilized microtubules, depletant, adenosine 5'-triphosphate (ATP), and clusters of kinesin-1 motors. We show that the microtubule-binding and unbinding kinetics of highly processive motor clusters set their ability to end-accumulate, which can drive polarity sorting of the microtubules and aster formation. We further demonstrate that the microscopic time scale of end-accumulation sets the emergent time scale of aster formation. Finally, we show that biochemical regulation is insufficient to fully explain the transition as generic aligning interactions through depletion, cross-linking, or excluded volume interactions can drive bundle formation despite end-accumulating motors. The extensile-to-contractile transition is well captured by a simple self-assembly model where nematic and polar aligning interactions compete to form either bundles or asters. Starting from a five-dimensional organization phase space, we identify a single control parameter given by the ratio of the different component concentrations that dictates the material-scale organization. Overall, this work shows that the interplay of biochemical and mechanical tuning at the microscopic level controls the robust self-organization of active cytoskeletal materials.

Hydrolyzed Reactive Red 195 adsorption on cellulose: Experimental and theoretical investigations

In this investigation, the mechanism of dye transfer during the mixed washing of natural cellulosic fabrics was elucidated through a comprehensive study of the hydrolysis of Reactive Red 195 (RR 195) and the subsequent adsorption of its hydrolysis products onto cellulose, approached both experimentally and theoretically. Initially, Reversed-phase high-performance liquid chromatography (RP-HPLC) was employed to identify the final products of Reactive Red 195 hydrolysis, collectively referred to as the unfixed dye substance ( UDS). This data provided theoretical insight into the hydrolysis mechanism of the dye. Following this identification, an adsorption kinetic model was established to delineate the interaction of the hydrolysis products with cellulose. Adsorption exhibited its maximal rate at a temperature of 60°C, under conditions of a wash bath ratio of 120:1 and a pH value of 7. Furthering the investigation, a molecular dynamics model was constructed to detail the adsorption process of these hydrolysis products on the hydrophobic surface Iβ(1 0 0) of cellulose within an aqueous environment. This model offered precise insights into the adsorption volume, kinetics, and mechanistic interaction at a molecular scale. Conclusive evidence from both theoretical analyses and experimental results suggested that the hydrolysis products, devoid of reactive groups, were incapable of chemically interacting with the hydroxyl groups inherent to cellulose. Instead, it was discerned that these products underwent a physical adsorption process onto the cellulose surface. Such adsorptive behavior is postulated to be a predominant factor influencing the dye transfer phenomenon in mixed washing conditions.

Chain stretching in brushes favors sequence recognition for nucleobase-functionalized flexible precise oligomers.

Six different flexible stereocontrolled oligo(triazole-urethane)s substituted by precise sequences of nucleobases or analogs are synthesized. Molecular dynamics simulations indicate that the flexibility of the backbone leads to unspecific complexation of pairs of oligomers, irrespective of the complementarity of their sequences. This is ascribed to the existence of other interactions between pairs of oligomers, as well as to the spatial blurring of the sequence order encoded in the chemical structure of the chain due to its flexibility. The same conclusions are drawn when investigating the irreversible adsorption of different probe oligomers onto a layer of target oligomers grafted by click chemistry in a mushroom configuration on a silicon substrate. In contrast, when the target oligomers are grafted in denser brush configurations, irreversible adsorption becomes more specific, with it being twice as probable that probe chains of complementary sequence would be irreversibly-bound to the layer of target chains than those of non-complementary sequence. This is ascribed to lateral excluded volume interactions between chains in the brush, leading to partial chain stretching and increased spatial preservation of the information contained in the monomer sequence of the chains. At even higher grafting densities, however, the penetration of the probe chains in the brush becomes increasingly difficult, resulting in a loss of binding efficiency. Our work thus demonstrates the adverse role of chain flexibility in the specificity of complexation between nucleobase-functionalized oligomers and provides directions for an improvement of specificity by tuning the grafting density of target chains on a substrate.

Capillary action and stationary currents in scalar active matter

Active matter consists of particles (motile microorganism or active colloids) that consume nutrients or fuel and convert it into a persistent motion, has received a lot of attention due to its intrinsic out-of-equilibrium character on the microscale [1]. The simplest representatives of active matter are spherically symmetric, active Brownian particles (ABPs) [2] without alignment, however, with excluded volume interactions [3,4].

Endocytosis efficiency and targeting ability by the cooperation of nanoparticles.

Cooperative wrapping of nanoparticles (NPs) with small sizes is an important pathway for the uptake of NPs by cell membranes. However, the cooperative wrapping efficiency and the effects of NPs' rigidity remain ambiguous. With the aid of computer simulations, we show that the complete wrapping mechanism of cooperative endocytosis is that the aggregation of NPs leads to greater wrapping forces than the single NP case, which triggers the increase of the wrapping degree and in turn further increases the wrapping forces until they are finally fully taken up. The effects of the NP size, initial distance, interaction strength, arrangement and stiffness on cooperative endocytosis were systematically studied. The cooperative wrapping efficiency increases as the NP radius increases. Hexagonal close packed NPs have the highest internalization efficiency. When the interactions are strong, softer NPs exhibit higher endocytosis efficiency. We further propose two strategies by combining NPs with different wrapping properties for targeting applications. By combining two NPs decorated with different types of ligands, the combination NPs can only be fully endocytosed by the cell membrane with two cognate types of receptors and adhere to the normal cell membrane with only one type of receptor. We also design composite NPs using a large NP non-covalently decorated with several small NPs. By harnessing the competition between the ligand-receptor interactions and the excluded volume interactions between the small NPs and the lipid membrane, the composite NPs have targeting ability towards the cancer cell membrane. The design concept of combining NPs with different wrapping properties for drug targeting applications may be very promising in biomedicine.

Development of soy protein isolate gels added with Tremella polysaccharides and psyllium husk powder as 3D printing inks for people with dysphagia.

The aim of this study was to investigate the feasibility of soy protein isolate (SPI) gels added with Tremella polysaccharides (TPs) and psyllium husk powder (PHP) as 3D printing inks for developing dysphagia-friendly food and elucidate the potential mechanism of TPs and PHP in enhancing the printing and swallowing performance of SPI gels. The results indicated that the SPI gels with a TP : PHP ratio of 3 : 7 could be effectively used as printing inks to manufacture dysphagia-friendly food. The addition of TPs increased the free water content, resulting in a decrease in the viscosity of the SPI gels, which, in turn, reduced the line width of the 3D-printed product and structural strength of the gel system. The addition of PHP increased disulfide bond interactions and excluded volume interactions, which determined the mechanical strength of SPI gels and increased the line width of the printed product. The synergistic effects between TPs and PHP improved the printing precision and structural stability. This study presents meaningful insights for the utilization of 3D printing in the creation of dysphagia-friendly food using protein-polysaccharide complexes.

Enhanced Coarse-Grained Molecular Dynamics Simulation with a Smoothed Hybrid Potential Using a Neural Network Model.

In all-atom (AA) molecular dynamics (MD) simulations, the rugged energy profile of the force field makes it challenging to reproduce spontaneous structural changes in biomolecules within a reasonable calculation time. Existing coarse-grained (CG) models, in which the energy profile is set to a global minimum around the initial structure, are unsuitable to explore the structural dynamics between metastable states far away from the initial structure without any bias. In this study, we developed a new hybrid potential composed of an artificial intelligence (AI) potential and minimal CG potential related to the statistical bond length and excluded volume interactions to accelerate the transition dynamics while maintaining the protein character. The AI potential is trained by energy matching using a diverse structural ensemble sampled via multicanonical (Mc) MD simulation and the corresponding AA force field energy, profile of which is smoothed by energy minimization. By applying the new methodology to chignolin and TrpCage, we showed that the AI potential can predict the AA energy with significantly high accuracy, as indicated by a correlation coefficient (R-value) between the true and predicted energies exceeding 0.89. In addition, we successfully demonstrated that CGMD simulation based on the smoothed hybrid potential can significantly enhance the transition dynamics between various metastable states while preserving protein properties compared to those obtained with conventional CGMD and AAMD.

Basic protein- and peptide-induced stabilization of long-loop DNA G-guadruplexes

The human genome contains many G-quadruplex-forming sequences, including sequences containing long single-stranded loops that are believed to be unfavorable for G-quadruplex formation. The intracellular environment of biological cells is crowded with proteins with charged surfaces. Understanding the effects of protein-rich environments is important for understanding the formation of G-quadruplexes in an intracellular environment. In this study, we investigated the structural stability of DNA G-quadruplexes in the presence of several types of globular proteins (lysozyme, cytochrome c, bovine serum albumin, myoglobin, histone proteins, and serum proteins), unstructured polypeptides (protamine and poly-l-lysine), and oligopeptides (RGG/RG-domain peptides and short repeated peptides). Thermal melting studies of G-quadruplex-forming oligonucleotides derived from the human telomeric repeat sequence revealed that environments containing high concentrations of proteins and peptides differently affected the G-quadruplex stability according to their loop lengths. We found that weak electrostatic interactions of G-quadruplex loops with basic proteins and peptides improved the stability of long-loop G-quadruplexes and the interactions were strengthened under crowded conditions simulated by dextran. The comparison of the effects of different types of proteins and peptides indicated that excluded volume interactions and structural flexibility of both DNA and polypeptide chains influenced the efficiency of their interactions. This study provides insights into long-loop G-quadruplex stability in a crowded intracellular environment and the recognition of G-quadruplexes by arginine-rich domains of G-quadruplex-binding proteins.

NIMG-70. TRACKING CELLULAR SOCIAL BEHAVIOR OF PATIENT-DERIVED PRIMARY CELL LINES TO GATHER NEW INSIGHTS FOR BETTER STRATIFICATION OF GLIOBLASTOMA PATIENTS

Abstract Glioblastoma is one of the most frequent and aggressive brain tumors. The average life of these patients is on average less than 15 months, due to the proliferation and invasiveness of the tumor cells, which not only constitute the tumor mass but which also infiltrate the normal parenchyma brain to form new cancerous sites. Knowing the specific behavior of the cell types that make up the tumor of every single patient, in terms of volume, shape, motility, and cell-cell interaction could be informative for patients’ tumor stratification. Here we developed a protocol that integrates imaging and image processing algorithms, to accurately and quantitatively identify the morphological and behavioral characteristics of tumor cells cultured in vitro and track their movement over time. This approach enables quantifying important biological processes such as cell migration and cell growth, both of which play a major role in the development of diseases. The cell tracking method combines segmentation methods with spatiotemporal optimization to analyze microscopy images. The method also determines various information about cell movements such as movement paths, speed, and distance covered. Knowing the behavior of the malignant glioma cells of a specific patient, in terms of shape and motility (e.g. direction and speed of movement), also in relation to other cells could be informative in the context of dynamic precision medicine. In this context, we created a model that integrates the characteristics of each patient's tumor cells and provides a new way of stratifying patients that can be correlated with clinical data.

Splay-induced order in systems of hard tapers.

The main objective of this work is to clarify the role that taper-shaped elongated molecules, i.e., molecules with one end wider than the other, can play in stabilizing orientational order. The focus is exclusively on entropy-driven self-organization induced by purely excluded volume interactions. Drawing an analogy to RM734 (4-[(4-nitrophenoxy)carbonyl]phenyl-2,4-dimethoxybenzoate), which is known to stabilize ferroelectric nematic (N_{F}) and nematic splay (N_{S}) phases, and assuming that molecular biaxiality is of secondary importance, we consider monodisperse systems composed of hard molecules. Each molecule is modeled using six collinear tangent spheres with linearly decreasing diameters. Through hard-particle, constant-pressure Monte Carlo simulations, we study the emergent phases as functions of the ratio between the smallest and largest diameters of the spheres (denoted as d) and the packing fraction (η). To analyze global and local molecular orderings, we examine molecular configurations in terms of nematic, smectic, and hexatic order parameters. Additionally, we investigate the radial pair distribution function, polarization correlation function, and the histogram of angles between molecular axes. The last characteristic is utilized to quantify local splay. The findings reveal that splay-induced deformations drive unusual long-range orientational order at relatively high packing fractions (η>0.5), corresponding to crystalline phases. When η<0.5, only short-range order is affected, and in addition to the isotropic liquid, only the standard nematic and smectic-A liquid crystalline phases are stabilized. However, for η>0.5, apart from the ordinary nonpolar hexagonal crystal, three additional frustrated crystalline polar blue phases with long-range splay modulation are observed: antiferroelectric splay crystal (Cr_{S}P_{A}), antiferroelectric double-splay crystal (Cr_{DS}P_{A}), and ferroelectric double-splay crystal (Cr_{DS}P_{F}). Finally, we employ Onsager-Parsons-Lee local density functional theory to investigate whether any sterically induced (anti)ferroelectric nematic or smectic-A type of ordering is possible for our system, at least in a metastable regime.

6 Posterior cerebral artery-defined white matter hyperintensities are associated with object domain memory and transentorhinal volume independently of global beta-amyloid burden

Objective:White matter hyperintensities (WMH) are a radiological marker of small vessel cerebrovascular disease that are related to cognition and memory decline in aging and Alzheimer’s disease (AD). However, the mechanisms that link WMH to memory impairment and whether they interact with or act independently of AD pathophysiology are unclear. The transentorhinal cortex (BA35) is among the earliest anatomical regions to show tau deposition and subsequent atrophy, and baseline posterior WMH is related to longitudinal cortical thinning of the entorhinal cortex. However, it is unclear whether regional WMH are related to BA35 volume specifically, and whether this relationship is influenced by amyloid-β (Aβ) burden. We hypothesized that WMH in the vascular territory of the posterior cerebral artery (PCA), which perfuses both posterior and medial temporal lobe regions, would be associated with reduced BA35 volume and with lower memory in older adults independently of Aβ.Participants and Methods:114 older adults without dementia, aged 60 to 98 years (mean (SD) = 78.31 (11.02), 71 (62.8%) women), were included. Regional WMH volumes were derived from T2-FLAIR images using ANTs, a vascular territory atlas and manual editing. Global Aβ was assessed with 18F-florbetapir PET, using SUVR of a cortical composite region (FBP mean SUVR) with a cerebellar reference region. Total transentorhinal (BA35) volume was derived using T1 and T2-weighted images using ASHS. To assess hippocampal pattern separation ability, an index of episodic memory, participants completed both object (MDT-O) and spatial (MDT-S) versions of a mnemonic discrimination task, with the lure discrimination index as the outcome. Using linear regressions, we first tested for associations among PCA-defined WMH, Aβ, BA35 volume, and MDT-S and MDT-O scores. We then tested whether the relationship between PCA-defined WMH and MDT-O performance was mediated by BA35 volume and whether this mediation was moderated by Aβ. All models adjusted for age, sex, and education.Results:PCA-defined WMH were related to higher FBP mean SUVR (b=0.287, p=0.042) and lower BA35 volume (b=-0.222, p=0.038). PCA-defined WMH were also negatively related to MDT-O performance (b=-0.229, p=0.044), but not to MDT-S (b=-0.171, p=0.118). FBP mean SUVR was not related to BA35 volume (b=-0.131, p=0.344) or MDT performance (MDT-S: b=-0.138, p=0.348; MDT-O: b=0.059, p=0.690). Furthermore, FBP mean SUVR did not interact with PCA-defined WMH to predict memory performance (interaction b=-0.039, p=0.973), nor BA35 volume (interaction b=-0.140, p=0.894). The association of PCA-defined WMH to MDT-O was fully mediated by BA35 volume (indirect effect b=-0.0005, 95% CI (-0.0014, -0.0003)). This mediation was not moderated by FBP mean SUVR (indirect effect b=-0.00001, 95% CI (-0.001, 0.001)).Conclusions:We found that PCA-defined WMH were related to memory performance in older adults, and this association is fully mediated by transentorhinal volume. While PCA-defined WMH are related to higher global Aβ burden, there is no interaction between PCA-defined WMH and Aβ on BA35 volume. These findings point to an amyloid-independent vascular pathway towards memory decline in aging and AD. Future work should examine whether the pathway linking PCA-defined WMH to transentorhinal cortex atrophy and subsequent memory decline is mediated by regional tau pathology.

Model-based dose optimization framework for bedaquiline, pretomanid and linezolid for the treatment of drug-resistant tuberculosis.

Bedaquiline, pretomanid and linezolid (BPaL) combination treatment against Mycobacterium tuberculosis is promising, yet safety and adherence concerns exist that motivate exploration of alternative dosing regimens. We developed a mechanistic modelling framework to compare the efficacy of the current and alternative BPaL treatment strategies. Pharmacodynamic models for each drug in the BPaL combination treatment were developed using in vitro time-kill data. These models were combined with pharmacokinetic models, incorporating body weight, lesion volume, site-of-action distribution, bacterial susceptibility and pharmacodynamic interactions to assemble the framework. The model was qualified by comparing the simulations against the observed clinical data. Simulations were performed evaluating bedaquiline and linezolid approved (bedaquiline 400 mg once daily [QD] for 14 days followed by 200 mg three times a week, linezolid 1200 mg QD) and alternative dosing regimens (bedaquiline 200 mg QD, linezolid 600 mg QD). The framework adequately described the observed antibacterial activity data in patients following monotherapy for each drug and approved BPaL dosing. The simulations suggested a minor difference in median time to colony forming unit (CFU)-clearance state with the bedaquiline alternative compared to the approved dosing and the linezolid alternative compared to the approved dosing. Median time to non-replicating-clearance state was predicted to be 15 days from the CFU-clearance state. The model-based simulations suggested that comparable efficacy can be achieved using alternative bedaquiline and linezolid dosing, which may improve safety and adherence in drug-resistant tuberculosis patients. The framework can be utilized to evaluate treatment optimization approaches, including dosing regimen and duration of treatment predictions to eradicate both replicating- and non-replicating bacteria from lung and lesions.

Accessible Molecular System Creator: Building Molecular Configurations Based on the Inaccessible Molecular Volume and Accessible Molecular Surface via Static Monte Carlo Sampling.

Monte Carlo (MC) stochastic sampling is a powerful tool in classical molecular simulations that directly connects the observable macroscopic properties of matter and the underlying atomistic interactions. This connection operates within the framework of the statistical mechanics proposed by Gibbs. Most MC simulations are "dynamic," creating statistical ensembles of microstates via a Markovian chain, where each microstate in the ensemble depends only on its previous microstate. Herein, we re-examine an alternative form of MC that generates ensemble members through a "static" approach, building molecular systems stepwise. The basic theory for such an approach traces back to Rosenbluth and Rosenbluth, who proposed "static" stepwise sampling of a polymeric chain. It is almost as old as the Metropolis importance sampling approach used in dynamic MC, although the latter has been considerably more popular than the former. Herein, we address the main obstacle in static MC that has hindered the widespread adoption of Rosenbluth-based approaches in atomistic simulations. The obstacle lies in mapping the molecular accessible volume for adding a molecule in a Rosenbluth-like static sampling of atomistic configurations. We demonstrate a breakthrough by leveraging the ability to analytically map the inaccessible molecular volume and the accessible molecular surface owing to interatomically excluded volume interactions. This advance substantially enhances the ability to create molecular samples using a Rosenbluth-like static building process. The proposed approach can be used as a tool for creating initial configurations in MC or molecular dynamics simulations─a field where Rosenbluth-like static building has been applied. Additionally, this approach can be used as the first step in a perturbation scheme that accurately estimates free energy differences by estimating the chemical work related to molecule addition, removal, or reinsertion within the context of free energy perturbation schemes employed in molecular simulations.

Rheological percolation, gel‐like behavior and electrical conductivity of multi‐walled carbon nanotubes filled ethylene‐vinyl acetate copolymer/acrylonitrile‐butadiene rubber nanocomposites

AbstractReasonable studies on the composite systems containing conductive nanoparticles are very important to manufacture the materials with physico‐mechanical tailor‐made properties. In this work, rheological percolation, gel‐like behavior and electrical properties of multi‐walled carbon nanotubes (MWCNTs) filled ethylene‐co‐vinyl acetate/acrylonitrile‐butadiene copolymer blends containing 0–7 wt% MWCNTs were studied. The Winter‐Chambon criterion validity was evaluated for physical gelation of the system. The rheological and electrical percolation threshold, gel point (Pg), relaxation exponent (n), gel strength (Sg), and the fractal dimension (df) at the gel point were calculated. The formation of physical gel and rheological percolation threshold were both found to occur at 1 wt% MWCNTs concentration. Based on the df value determined, it was revealed that the system behaved similar to the one in which the excluded volume interactions were nearly screened. It was also found that the storage modulus (G′) near the Pg followed a power‐law scaling relationship in the form where is the distance from Pg. The electrical conductivity of the nanocomposites increased with the increase in MWCNTs loading after the nanofillers content surpassed a certain value. A schematic model was proposed to demonstrate the variation of electrical conduction with the increase in MWCNTs concentration. The excluded volume and hard‐core models were also employed to estimate the average aspect ratio of the nanofillers embedded in the system.Highlights Morphology and gel‐like behavior of EVA/NBR/MWCNTs system were studied Winter‐Chambon criterion was found to be valid for the gelation of the system Rheological percolation and gel point were occurred at the same MWCNTs loading It was found excluded volume interactions were nearly screened at gel point A schematic model for microstructure development was suggested for the system

Intrinsic viscosity and dielectric relaxation of ring polymers in dilute solutions.

The absence of chain ends makes ring polymers distinctly different from their linear analogues. The intrinsic viscosity, complex viscosity and the dielectric relaxation of ring polymers are investigated within the tenets of the optimized Rouse-Zimm theory. The distance dependent excluded volume interactions (EVIs) are obtained from Flory's mean field theory. The hydrodynamic interactions (HIs) between the pairs of monomers are estimated using the preaveraged Oseen tensor. The intrinsic viscosity of linear and ring polymers both with and without EVI are compared as a function of ring size. A monotonically increasing trend of the intrinsic viscosity is observed in both cases. The intrinsic viscosity of both linear and ring polymers both with and without EVI show a very good agreement with the experimental results of polystyrene over a wide range of molecular weights in both good and theta solvents, respectively. The fractal dimensions of the ring polymers with EVI lie between that of a random walk and a self-avoiding walk model of linear polymers in three dimensions. The ring size increases with EVI and the effect of EVI is stronger on larger rings than that on smaller rings. The dielectric relaxation follow a connectivity independent universal scaling behavior at low and high frequency regions. The imaginary part of the complex dielectric susceptibility displays a local maxima in the intermediate frequency region, which reveals a structure dependent behavior of the rings. The theoretically calculated dielectric loss of ring polymers with HI matches well with those obtained from experiments.

Simplified Equilibrium Model for Exploring the Combined Influences of Concentration, Aggregate Shape, Excluded Volume, and Surface Adsorption upon Aggregation Propensity and Distribution of Globular Macromolecules.

A mesoscopic model for the equilibrium self-association of a globular macromolecule that may form oligomers of various shapes and unlimited sizes is presented. Allowance is made within this model for the effects of variation in the free energy of subunit contact within an oligomer of specified size and different shapes, the free energy of adsorption of an oligomer of specified size and shape to a planar surface, and the free energy of nonspecific excluded volume interaction between an oligomer of specified size and shape and an inert species occupying a specified fraction of total volume. The model is analytically soluble and permits rapid calculation and analysis of the effects of variation in each of the three free energy parameters upon the concentration dependence of the weight-average stoichiometry of the oligomer, the fraction of total macromolecule that is adsorbed, and the fraction of differently shaped oligomers that are adsorbed and in free solution.

Physical modeling of ribosomes along messenger RNA: Estimating kinetic parameters from ribosome profiling experiments using a ballistic model.

Gene expression is the synthesis of proteins from the information encoded on DNA. One of the two main steps of gene expression is the translation of messenger RNA (mRNA) into polypeptide sequences of amino acids. Here, by taking into account mRNA degradation, we model the motion of ribosomes along mRNA with a ballistic model where particles advance along a filament without excluded volume interactions. Unidirectional models of transport have previously been used to fit the average density of ribosomes obtained by the experimental ribo-sequencing (Ribo-seq) technique in order to obtain the kinetic rates. The degradation rate is not, however, accounted for and experimental data from different experiments are needed to have enough parameters for the fit. Here, we propose an entirely novel experimental setup and theoretical framework consisting in splitting the mRNAs into categories depending on the number of ribosomes from one to four. We solve analytically the ballistic model for a fixed number of ribosomes per mRNA, study the different regimes of degradation, and propose a criterion for the quality of the inverse fit. The proposed method provides a high sensitivity to the mRNA degradation rate. The additional equations coming from using the monosome (single ribosome) and polysome (arbitrary number) ribo-seq profiles enable us to determine all the kinetic rates in terms of the experimentally accessible mRNA degradation rate.

Not Always Sticky: Specificity of Protein Stabilization by Sugars Is Conferred by Protein-Water Hydrogen Bonds.

Solutes added to buffered solutions directly impact protein folding. Protein stabilization by cosolutes or crowders has been shown to be largely driven by protein-cosolute volume exclusion complemented by chemical and soft interactions. By contrast to previous studies that indicate the invariably destabilizing role of soft protein-sugar attractions, we show here that soft interactions with sugar cosolutes are protein-specific and can be stabilizing or destabilizing. We experimentally follow the folding of two model miniproteins that are only marginally stable but in the presence of sugars and polyols fold into representative and distinct secondary structures: β-hairpin or α-helix. Our mean-field model reveals that while protein-sugar excluded volume interactions have a similar stabilizing effect on both proteins, the soft interactions add a destabilizing contribution to one miniprotein but further stabilize the other. Using molecular dynamics simulations, we link the soft protein-cosolute interactions to the weakening of direct protein-water hydrogen bonding due to the presence of sugars. Although these weakened hydrogen bonds destabilize both the native and denatured states of the two proteins, the resulting contribution to the folding free energy can be positive or negative depending on the amino acid sequence. This study indicates that the significant variation between proteins in their soft interactions with sugar determines the specific response of different proteins, even to the same sugar.