Chain Fluctuations Research Articles

САМООЧИСНИЙ ФІЛЬТР ДЛЯ ЗАМКНУТИХ ГІДРОСИСТЕМ СІЛЬСЬКОГОСПОДАРСЬКОГО ОБЛАДНАННЯ

The issue of increasing the reliability and durability of hydraulic units of closed hydraulic systems of agricultural equipment is considered, due to better cleaning of the working fluid by filtration units. The design of a self-cleaning filter with hydraulic automatic control of backwashing of slotted filtration elements with a counterflow of the working fluid is proposed. A special stand has been developed for simulating the operation of a self-cleaning filter of closed hydraulic systems of agricultural equipment. Experimental studies on a special stand confirmed the efficiency of the proposed design and made it possible to identify its main advantages in comparison with domestic and foreign counterparts. Based on the analysis of transient processes with increased pressure pulsation of agricultural equipment of a closed hydraulic drive, the actual pressure drop at which automatic flushing is triggered was established, compared with the calculated one, in which it was impossible to take into account such real factors as friction in the sealing units, the characteristics of the springs, distortions, tightness of valve pairs, fluctuations in dimensional chains. The most optimal operating mode of auto-washing equipment with a choke diameter of 1.0 mm has been determined. The auto-washing equipment was switched on at a pressure drop of 1.5 MPa (15 atm) and in an improved mode – pressure pulsations with an amplitude of 2 MPa (20 atm) when the auto-wash was turned off decreased in time to 0.12 s. It is noted that the developed self-cleaning filter for closed hydraulic systems of agricultural equipment will improve the reliability and increase the service life of the elements of hydraulic units and the machine itself as a whole.

Virtual screening and molecular dynamics study of approved drugs as inhibitors of spike protein S1 domain and ACE2 interaction in SARS-CoV-2

BackgroundThe receptor binding domain (RBD) of spike protein S1 domain SARS-CoV-2 plays a key role in the interaction with ACE2, which leads to subsequent S2 domain mediated membrane fusion and incorporation of viral RNA into host cells. In this study we tend to repurpose already approved drugs as inhibitors of the interaction between S1-RBD and the ACE2 receptor. Methods2456 approved drugs were screened against the RBD of S1 protein of SARS-CoV-2 (target PDB ID: 6M17). As the interacting surface between S1-RBD and ACE2 comprises of bigger region, the interacting surface was divided into 3 sites on the basis of interactions (site 1, 2 and 3) and a total of 5 grids were generated (site 1, site 2, site 3, site 1+site 2 and site 2+site 3). A virtual screening was performed using GLIDE implementing HTVS, SP and XP screening. The top hits (on the basis of docking score) were further screened for MM-GBSA. All the top hits were further evaluated in molecular dynamics studies. Performance of the virtual screening protocol was evaluated using enrichment studies. Resultand discussion: We performed 5 virtual screening against 5 grids generated. A total of 42 compounds were identified after virtual screening. These drugs were further assessed for their interaction dynamics in molecular dynamics simulation. On the basis of molecular dynamics studies, we come up with 10 molecules with favourable interaction profile, which also interacted with physiologically important residues (residues taking part in the interaction between S1-RBD and ACE2. These are antidiabetic (acarbose), vitamins (riboflavin and levomefolic acid), anti-platelet agents (cangrelor), aminoglycoside antibiotics (Kanamycin, amikacin) bronchodilator (fenoterol), immunomodulator (lamivudine), and anti-neoplastic agents (mitoxantrone and vidarabine). However, while considering the relative side chain fluctuations when compared to the S1-RBD: ACE2 complex riboflavin, fenoterol, cangrelor and vidarabine emerged out as molecules with prolonged relative stability. ConclusionWe identified 4 already approved drugs (riboflavin, fenoterol, cangrelor and vidarabine) as possible agents for repurposing as inhibitors of S1:ACE2 interaction. In-vitro validation of these findings are necessary for identification of a safe and effective inhibitor of S1: ACE2 mediated entry of SARS-CoV-2 into the host cell.

Heterogeneous Polymer Dynamics Explored Using Static 1H NMR Spectra.

NMR spectroscopy continues to provide important molecular level details of dynamics in different polymer materials, ranging from rubbers to highly crosslinked composites. It has been argued that thermoset polymers containing dynamic and chemical heterogeneities can be fully cured at temperatures well below the final glass transition temperature (Tg). In this paper, we described the use of static solid-state 1H NMR spectroscopy to measure the activation of different chain dynamics as a function of temperature. Near Tg, increasing polymer segmental chain fluctuations lead to dynamic averaging of the local homonuclear proton-proton (1H-1H) dipolar couplings, as reflected in the reduction of the NMR line shape second moment (M2) when motions are faster than the magnitude of the dipolar coupling. In general, for polymer systems, distributions in the dynamic correlation times are commonly expected. To help identify the limitations and pitfalls of M2 analyses, the impact of activation energy or, equivalently, correlation time distributions, on the analysis of 1H NMR M2 temperature variations is explored. It is shown by using normalized reference curves that the distributions in dynamic activation energies can be measured from the M2 temperature behavior. An example of the M2 analysis for a series of thermosetting polymers with systematically varied dynamic heterogeneity is presented and discussed.

The Dynamism of Intrinsically Disordered Proteins in Liquid-Liquid Phase Separation

A growing body of research has revealed that living cells contain a variety of membrane-less organelles that are formed via liquid phase condensation of intrinsically disordered proteins/regions (IDPs/IDRs) that engage in a multitude of transient, non-covalent interactions resulting in liquid-liquid phase separation into mesoscopic liquid-like compartments. These liquid-like condensates can undergo liquid-to-solid maturation into pathological solid-like aggregates in deadly human diseases. By utilizing a diverse array of unique, sensitive, and time-resolved spectroscopic tools, we have been able to directly capture an intriguing symphony of molecular events involving protein unwinding and fluctuations during phase separation. We show that unusual conformational expansion events coupled with extensive solvation and rapid large-scale conformational fluctuations drive liquid-liquid phase separation of intrinsically disordered tau that is linked to Alzheimer's disease. Using pyrene excimer as a spectroscopic intramolecular ruler, we directly monitored the chain unraveling during phase transition. These expanded chains participate in critical interchain interactions within the droplets. Our solvent accessibility measurements revealed a greater extent of chain solvation within the droplets compared to the dispersed phase. Using picosecond time-resolved fluorescence depolarization measurements, we directly captured rapid backbone dihedral fluctuations that can mediate temporal making-and-breaking of noncovalent intermolecular contacts. These dynamic events govern transient noncovalent contacts and maintain the inner fluidity that is crucial for liquid-like condensates. Our observations, together with the existing and emerging polymer theories, suggest that such molecular shapeshifting events involving chain expansion, solvation, and fluctuations can provide additional favorable free energies to overcome the entropy of mixing, and therefore, can promote the phase transition. We are currently studying phase separation of another amyloidogenic IDP comprising the low-complexity regions. Results from these studies providing unique molecular insights into liquid phase condensation and liquid-to-solid maturation will also be discussed.

Adsorption of a Helical Filament Subject to Thermal Fluctuations.

We consider semiflexible chains governed by preferred curvature and twist and their flexural and twist moduli. These filaments possess a helical rather than straight three-dimensional (3D) ground state and we call them helical filaments (H-filament). Depending on the moduli, the helical shape may be smeared by thermal fluctuations. Secondary superhelical structures are expected to form on top of the specific local structure of biofilaments, as is documented for vimentin. We study confinement and adsorption of helical filaments utilizing both a combination of numerical simulations and analytical theory. We investigate overall chain shapes, transverse chain fluctuations, loop and tail distributions, and energy distributions along the chain together with the mean square average height of the monomers . The number fraction of adsorbed monomers serves as an order parameter for adsorption. Signatures of adsorbed helical polymers are the occurrence of 3D helical loops/tails and spiral or wavy quasi-flat shapes. None of these arise for the Worm-Like-Chain, whose straight ground state can be embedded in a plane.

Resilience assessment of the lithium supply chain in China under impact of new energy vehicles and supply interruption

Abstract The development of new energy vehicles had a huge impact on lithium demand under the framework of the lithium supply chain, and geopolitical changes have increased the risk of lithium supply interruption. Does the lithium supply chain have the coping ability under the demand impact of new energy vehicles and the risk of supply interruption? Can some improvement measures improve the coping ability of the lithium supply chain? In this paper, the system dynamic modeling is used method to evaluate the supply-chain resilience; make the price, supply and demand systems be the three resilient mechanisms of the lithium supply chain; and set demand impact, supply interrupt, and three enhancement measures as the model scenes. The simulation results show that the lithium supply chain is less resilient under the impact of new energy vehicles. Furthermore, the resilience of the lithium supply chain is good under the risk of short-term supply interruption, but worse under long-term supply interruption. Finally, promoting a design for recycling has the most obvious improvement in coping ability with the lithium supply chain, with reserve stockpile and drawdown focused more on adjusting supply chain fluctuations and; material substitution has only a slight improvement in supply-chain resilience.

Polymer gel with a flexible and highly ordered three-dimensional network synthesized via bond percolation.

Gels are a soft elastic material consisting of a three-dimensional polymer network with nanometer-sized pores and are used in a variety of applications. However, gel networks typically have a substantial level of defects because the network formation reaction proceeds stochastically. In this study, we present a general scheme to fabricate gels with extremely low levels of defects by applying geometric constraints into pregel solution based on the "bond percolation" concept. In the formed gel, stationary laser speckles, which are an indicator of spatial defects, were not observed at all. In addition, we found that the concentration fluctuations of the polymer chains were ergodic across the whole gel network. In such a homogeneous gel, both the spatial and temporal correlations of polymer chains are the same before and after gelation.

Solution Structure and Conformational Flexibility in the Active State of the Orange Carotenoid Protein. Part II: Quasielastic Neutron Scattering.

Orange carotenoid proteins (OCPs), which are protecting cyanobacterial light-harvesting antennae from photodamage, undergo a pronounced structural change upon light absorption. In addition, the active state is anticipated to boost a significantly higher molecular flexibility similar to a "molten globule" state. Here, we used quasielastic neutron scattering to directly characterize the vibrational and conformational molecular dynamics of OCP in its ground and active states, respectively, on the picosecond time scale. At a temperature of 100 K, we observe mainly (vibronic) inelastic features with peak energies at 5 and 6 meV (40 and 48 cm-1, respectively). At physiological temperatures, however, two (Lorentzian) quasielastic components represent localized protein motions, that is, stochastic structural fluctuations of protein side chains between various conformational substates of the protein. Global diffusion of OCP is not observed on the given time scale. The slower Lorentzian component is affected by illumination and can be well-characterized by a jump-diffusion model. While the jump diffusion constant D is (2.82 ± 0.01) × 10-5 cm2/s at 300 K in the ground state, it is increased by ∼20% to (3.48 ± 0.01) × 10-5 cm2/s in the active state, revealing a strong enhancement of molecular mobility. The increased mobility is also reflected in the average atomic mean square displacement ⟨u2⟩; we determine a ⟨u2⟩ of 1.47 ± 0.05 Å in the ground state, but 1.86 ± 0.05 Å in the active state (at 300 K). This effect is assigned to two factors: (i) the elongated structure of the active state with two widely separated protein domains is characterized by a larger number of surface residues with a concomitantly higher degree of motional freedom and (ii) a larger number of hydration water molecules bound at the surface of the protein. We thus conclude that the active state of the orange carotenoid protein displays an enhanced conformational dynamics. The higher degree of flexibility may provide additional channels for nonradiative decay so that harmful excess energy can be more efficiently converted to heat.

Structure of Ultrafine Bubbles and Their Effects on Protein and Lipid Membrane Structures Studied by Small- and Wide-Angle X-ray Scattering.

Ultrafine bubbles (UFBs) are defined as small gas-filled bubbles with a diameter smaller than 1 μm. UFBs are stable for several weeks in aqueous solutions due to their small size. Although the mechanism of the stability of UFBs remains under intensive investigation, industrial applications of UFBs have recently arisen in various fields such as agricultural and fishery industries and medical therapy. The relevance of ions (protons and hydroxide anions) in UFB solutions has been discussed; however, the mechanism underlying the behavior of UFBs is still ambiguous and there is little direct evidence of the effect of UFBs on biological materials. This study deals with gaseous UFBs in aqueous solutions. Using small- and wide-angle X-ray scattering, we have investigated the structures of UFBs (air-UFBs, O2-UFBs, and N2-UFBs) and their effect on protein and lipid membrane structures. X-ray scattering and modeling data suggest that UFBs present a dynamic diffusive boundary (interface) due to the continuous release and absorption of gas. UFBs were found to not affect the structures of proteins at all hierarchal structure levels (from quaternary to tertiary, to internal, to secondary), whereas they did influence the packing and fluctuation of the hydrocarbon chains in the liposomes but not their shapes.

The stick-slip mechanism for granular flow lubrication

PurposeGranular flow lubrication is developed in recent years as a new lubrication method which can be used in extreme environments, while the stick-slip mechanisms of granular flow lubrication are an urgent obstacle remains unsolved in fully establishing the granular flow lubrication theory.Design/methodology/approachA granular flow lubrication research model is constructed by the discrete element method. Using this numerical model, the mesoscopic and macroscopic responses of stick-slip that influenced by the shear velocity, and the influence of the shear velocity and the normal pressure on the vertical displacement are studied.FindingsResearch results show that movement states of granular flow lubrication medium gradually transform from the stick-slip state to the sliding state with increased shear velocity, in which these are closely related to the fluctuations of force chains and friction coefficients between granules. The stick-slip phenomenon comes up at lower shear velocity prior to the appearance of granular lift-off between the two friction pair, which comes up at higher shear velocity. Higher normal pressure restrains the dilatation of the granular flow lubrication medium, which in turn causes a decrease in the displacement.Originality/valueThese findings reveal the stick-slip mechanism of granular flow lubrication and can also offer the helpful reference for the design of the new granular lubrication bearing.

Current fluctuations in boundary-driven quantum spin chains

Boundary-driven spin chains are paradigmatic non-equilibrium systems in both classical and quantum settings. In general it may not be possible to distinguish classical from quantum transport through monitoring the mean current, as both ballistic as well as diffusive regimes occur in either setting. Here we show that genuine quantum features become manifest in large fluctuations which allow a discrimination between classical and quantum transport: in the classical case, realizations that are characterized by atypically large boundary activity are associated with larger than typical currents, i.e. an enhanced number of events at the boundaries goes together with a large current. Conversely, in the quantum case the Zeno effect leads to the suppression of current in trajectories with large activity at the boundary. We analyze how these different dynamical regimes are reflected in the structure of rare fluctuations. We show furthermore that realizations supporting a large current are generated via weak long-range correlations within the spin chain, typically associated with hyperuniformity.

AWSEM-IDP: A Coarse-Grained Force Field for Intrinsically Disordered Proteins.

The associative memory, water-mediated, structure and energy model (AWSEM) has been successfully used to study protein folding, binding, and aggregation problems. In this work, we introduce AWSEM-IDP, a new AWSEM branch for simulating intrinsically disordered proteins (IDPs), where the weights of the potentials determining secondary structure formation have been finely tuned, and a novel potential is introduced that helps to precisely control both the average extent of protein chain collapse and the chain's fluctuations in size. AWSEM-IDP can efficiently sample large conformational spaces, while retaining sufficient molecular accuracy to realistically model proteins. We applied this new model to two IDPs, demonstrating that AWSEM-IDP can reasonably well reproduce higher-resolution reference data, thus providing the foundation for a transferable IDP force field. Finally, we used thermodynamic perturbation theory to show that, in general, the conformational ensembles of IDPs are highly sensitive to fine-tuning of force field parameters.

Microglobule formation and a microscopic order parameter monitoring the phase transition of aqueous poly( N -isopropylacrylamide) solution

The coil-to-globule transition of poly($N$-isopropylacrylamide) (pNIPAm) in water is generally believed to be driven by hydrophobic interaction between the isopropyl groups of its side chains. However, it is still unclear how dehydration and critical fluctuations of the polymer chains are correlated. Here, we use small- and wide-angle x-ray scattering and dielectric relaxation spectroscopy to cover a wide range of the relevant length and time scales, enabling us to grasp an overall picture of this phase transition. We find that the hydration number of pNIPAm decreases only moderately with temperature up to about 6 K below its spinodal temperature ${T}_{\mathrm{S}}$, but then drops steeply on approaching ${T}_{\mathrm{S}}$. This rapid dehydration is coupled to a mean-field-like power-law divergence of the correlation length $\ensuremath{\xi}$, representing fluctuations of the density order parameter. Real-space decoding of an observed interference peak reveals partial-globule formation even far below ${T}_{\mathrm{S}}$ and demonstrates that the polymer-rich phase above ${T}_{\mathrm{S}}$ can be understood as a high-density assembly of the microglobules. Strikingly, condensation of the microglobules and the divergence of $\ensuremath{\xi}$ do not run parallel. Instead, the condensation occurs only above ${T}_{\mathrm{S}}$ and is completed about 6 K above ${T}_{\mathrm{S}}$. The local number density of the microglobules, exhibiting a steplike increase just above ${T}_{\mathrm{S}}$, should be identified as an additional microscopic order parameter governing the phase transition of pNIPAm.

Sampling rare fluctuations of discrete-time Markov chains.

We describe a simple method that can be used to sample the rare fluctuations of discrete-time Markov chains. We focus on the case of Markov chains with well-defined steady-state measures, and derive expressions for the large-deviation rate functions (and upper bounds on such functions) for dynamical quantities extensive in the length of the Markov chain. We illustrate the method using a series of simple examples, and use it to study the fluctuations of a lattice-based model of active matter that can undergo motility-induced phase separation.

Mapping of uncertainty relations between continuous and discrete time.

Lower bounds on fluctuations of thermodynamic currents depend on the nature of time, discrete or continuous. To understand the physical reason, we compare current fluctuations in discrete-time Markov chains and continuous-time master equations. We prove that current fluctuations in the master equations are always more likely, due to random timings of transitions. This comparison leads to a mapping of the moments of a current between discrete and continuous time. We exploit this mapping to obtain uncertainty bounds. Our results reduce the quests for uncertainty bounds in discrete and continuous time to a single problem.

An empirical study of demand forecasting of non-volatile memory for smart production of semiconductor manufacturing

As high-speed computing is crucial to empower intelligent manufacturing for Industry 4.0, non-volatile memory (NVM) is critical semiconductor component of the cloud and data centre for the infrastructures. The NVM manufacturing is capital intensive, in which capacity utilisation significantly affects the capital effectiveness and profitability of semiconductor companies. Since capacity migration and expansion involve long lead times, demand forecasting plays a critical role for smart production of NVM manufacturers for revenue management. However, the shortening product life cycles of integrated circuits (IC), the fluctuations of semiconductor supply chains, and uncertainty involved in demand forecasting make the present problem increasingly difficult in the consumer electronics era. Focusing on the realistic needs of NVM demand forecasting, this study aims to develop a decision framework that integrates an improved technology diffusion model and a proposed adjustment mechanism to incorporate domain insights. An empirical study was conducted in a leading semiconductor company for validation. A comparison of alternative approaches is also provided. The results have shown the practical viability of the proposed approach.

Origin of diverse time scales in the protein hydration layer solvation dynamics: A simulation study.

In order to inquire the microscopic origin of observed multiple time scales in solvation dynamics, we carry out several computer experiments. We perform atomistic molecular dynamics simulations on three protein-water systems, namely, lysozyme, myoglobin, and sweet protein monellin. In these experiments, we mutate the charges of the neighbouring amino acid side chains of certain natural probes (tryptophan) and also freeze the side chain motions. In order to distinguish between different contributions, we decompose the total solvation energy response in terms of various components present in the system. This allows us to capture the interplay among different self- and cross-energy correlation terms. Freezing the protein motions removes the slowest component that results from side chain fluctuations, but a part of slowness remains. This leads to the conclusion that the slow component approximately in the 20-80 ps range arises from slow water molecules present in the hydration layer. While the more than 100 ps component has multiple origins, namely, adjacent charges in amino acid side chains, hydrogen bonded water molecules and a dynamically coupled motion between side chain and water. In addition, the charges enforce a structural ordering of nearby water molecules and helps to form a local long-lived hydrogen bonded network. Further separation of the spatial and temporal responses in solvation dynamics reveals different roles of hydration and bulk water. We find that the hydration layer water molecules are largely responsible for the slow component, whereas the initial ultrafast decay arises predominantly (approximately 80%) due to the bulk. This agrees with earlier theoretical observations. We also attempt to rationalise our results with the help of a molecular hydrodynamic theory that was developed using classical time dependent density functional theory in a semi-quantitative manner.

The Effects of Alkyl Chain Combinations on the Structural and Mechanical Properties of Biomimetic Ion Pair Amphiphile Bilayers.

Ion pair amphiphile (IPA), a lipid-like complex composed of a pair of cationic and anionic surfactants, has great potentials in various pharmaceutical applications. In this work, we utilized molecular dynamics (MD) simulation to systematically examine the structural and mechanical properties of the biomimetic bilayers consist of alkyltrimethyl-ammonium-alkylsulfate (CmTMA+-CnS−) IPAs with various alkyl chain combinations. Our simulations show an intrinsic one-atom offset for the CmTMA+ and CnS− alignment, leading to the asymmetric index definition of ΔC = m − (n + 1). Larger |ΔC| gives rise to higher conformational fluctuations of the alkyl chains with the reduced packing order and mechanical strength. In contrast, increasing the IPA chain length enhances the van der Waals interactions within the bilayer and thus improves the bilayer packing order and mechanical properties. Further elongating the CmTMA+-CnS− alkyl chains to m and n ≥ 12 causes the liquid disorder to gel phase transition of the bilayer at 298 K, with the threshold membrane properties of 0.45 nm2 molecular area, deuterium order parameter value of 0.31, and effective bending rigidity of 20 kBT, etc. The combined results provide molecular insights into the design of biomimetic IPA bilayers with wide structural and mechanical characteristics for various applications.

Strong Stretching of Poly(ethylene glycol) Brushes Mediated by Ionic Liquid Solvation.

We have measured forces between mica surfaces coated with a poly(ethylene glycol) (PEG) brush solvated by a vacuum-dry ionic liquid, 1-ethyl-3-methyl imidazolium bis(trifluoromethylsulfonyl)imide, with a surface forces apparatus. At high grafting density, the solvation mediated by the ionic liquid causes the brush to stretch twice as much as in water. Modeling of the steric repulsion indicates that PEG behaves as a polyelectrolyte; the hydrogen bonding between ethylene glycol and the imidazolium cation seems to effectively charge the polymer brush, which justifies the strong stretching. Importantly, under strong polymer compression, solvation layers are squeezed out at a higher rate than for the neat ionic liquid. We propose that the thermal fluctuations of the PEG chains, larger in the brush than in the mushroom configuration, maintain the fluidity of the ionic liquid under strong compression, in contrast to the solid-like squeezing-out behavior of the neat ionic liquid. This is the first experimental study of the behavior of a polymer brush solvated by an ionic liquid under nanoconfinement.

Relation between Cross-Link Fluctuations and Elasticity in Entangled Polymer Networks

Computer simulation data on junction fluctuations in end-linked model networks are analyzed using the framework of the constraint junction model and the slip tube model for entangled networks. It is argued that cross-linking freezes in conformational fluctuations of chains and cross-links, which creates a small preload of entangled strands. This can be modeled using a “confinement degree of polymerization” Nc(N) with a weak dependence on the degree of polymerization N. The confined motion of network junctions with f active connections to the network is well described by using the exact solution of the constrained junction model with a constraining term that is given by the superposition of f/2 entanglement tubes with confinement Nc(N). It is shown that the modulus of end-linked model networks is the sum of a phantom and an entanglement contribution, whereby the entanglement contribution shows the same correction Nc(N) as both the cross-link fluctuations and the time average bond orientations. The results ...