Brownian Ratchet Research Articles

Microbial transport and dispersion in heterogeneous flows created by pillar arrays

Swimming microbes, such as bacteria and algae, live in diverse habitats including soil, seawater, and the human body. The habitats are characterized by structural boundaries and heterogeneous fluid flows. Although in recent decades much progress has been made in understanding the Brownian ratchet motion of microbes and their hydrodynamic interactions with the wall, the complex interplay between the structural and fluid environment with self-propelling microbial motion still remains elusive. Here, we developed a Langevin model to simulate and investigate the transport and dispersion of microbes in periodic pillar arrays. By tracing the spatiotemporal evolution of microbial trajectories, we show that a no-slip pillar surface induces local fluid shear, which redirects microbial movements. In the vicinity of pillars, looping trajectories and slow motion lead to a transient accumulation and sluggish transport of microbes. Several modes of microscopic motion, including swinging, zigzag, and adhesive motion, were observed. In an asymmetric pillar array, adjacent downstream pillars provide geometric guidance such that the microbial population has a deterministic shift perpendicular to the flow direction. Moreover, the effects of the topology of the pillar array, fluid flow properties, and microbial properties on microbial advection and dispersion in a pillar array were quantitatively analyzed. Our results highlight the importance of surrounding structures and flow on microbial transport and distribution, and these should be carefully considered in the study of microbial processes.

Experimental investigation on thermal characteristics of a novel mesh flat-plate heat receiver in a solar power tower system

In solar power tower systems, the heating surface of a heat receiver is prone to local overheating, thermal fatigue, and thermal ratcheting under nonstationary, nonuniform, and high-heat-flow-density loads, resulting in failure of the heat receiver. Therefore, this paper proposes a novel high-temperature, mesh, flat-plate heat receiver (FPHR) comprising multiple micro heat pipe loops. A series of tests were conducted to investigate the heat transfer characteristics and cooling start-up performance of the mesh FPHR. The results indicate that the larger cooling rates can reduce successful start-up times by more than 12%, and the FPHR has excellent isothermal performance (<35.05 °C) and heat transfer performance, which can withstand high-heat-flow-density loads and effectively prevent the harm caused by thermal stress. In addition, the nonuniform heating condition has a greater impact on the isothermal performance of FPHR, and the maximum temperature difference of the heat absorption surface with the change of the tilt angle is only reduced by 2.03 °C. The efficiency of the FPHR can exceed 83.98% and the air outlet temperature can exceed 714.5 °C. The results will contribute to the further development of heat receivers used in solar power tower systems.

Molecular-sized outward-swinging gate: Experiment and theoretical analysis of a locally nonchaotic barrier.

We investigate the concept of molecular-sized outward-swinging gate, which allows for entropy decrease in an isolated system. The theoretical analysis, the Monte Carlo simulation, and the direct solution of governing equations all suggest that under the condition of local nonchaoticity, the probability of particle crossing is asymmetric. It is demonstrated by an experiment on a nanoporous membrane one-sidedly surface-grafted with bendable organic chains. Remarkably, through the membrane, gas spontaneously and repeatedly flows from the low-pressure side to the high-pressure side. While this phenomenon seems counterintuitive, it is compatible with the principle of maximum entropy. The locally nonchaotic gate interrupts the probability distribution of the local microstates, and imposes additional constraints on the global microstates, so that entropy reaches a nonequilibrium maximum. Such a mechanism is fundamentally different from Maxwell's demon and Feynman's ratchet, and is consistent with microscopic reversibility. It implies that useful work may be produced in a cycle from a single thermal reservoir. A generalized form of the second law of thermodynamics is proposed.

Distance-dependent inhibition of translation initiation by downstream out-of-frame AUGs reveals that ribosome scans in a Brownian ratchet process

Distance-dependent inhibition of translation initiation by downstream out-of-frame AUGs reveals that ribosome scans in a Brownian ratchet process

Distance-dependent inhibition of translation initiation by downstream out-of-frame AUGs reveals that ribosome scans in a Brownian ratchet process

Distance-dependent inhibition of translation initiation by downstream out-of-frame AUGs reveals that ribosome scans in a Brownian ratchet process

Distance-dependent inhibition of translation initiation by downstream out-of-frame AUGs is consistent with a Brownian ratchet process for ribosome scanning

Distance-dependent inhibition of translation initiation by downstream out-of-frame AUGs is consistent with a Brownian ratchet process for ribosome scanning

Distance-dependent inhibition of translation initiation by downstream out-of-frame AUGs reveals that ribosome scans in a Brownian ratchet process

Distance-dependent inhibition of translation initiation by downstream out-of-frame AUGs reveals that ribosome scans in a Brownian ratchet process

Distance-dependent inhibition of translation initiation by downstream out-of-frame AUGs is consistent with a Brownian ratchet process for ribosome scanning

Distance-dependent inhibition of translation initiation by downstream out-of-frame AUGs is consistent with a Brownian ratchet process for ribosome scanning

Distance-dependent inhibition of translation initiation by downstream out-of-frame AUGs is consistent with a Brownian ratchet process for ribosome scanning

Distance-dependent inhibition of translation initiation by downstream out-of-frame AUGs is consistent with a Brownian ratchet process for ribosome scanning

Creep and thermal ratcheting characterization of polytetrafluoroethylene-based gasket materials

Characterization of Teflon polymer based gaskets under expedited aging is the objective of this work. Teflon gaskets are exploited frequently as a replacement to asbestos fiber gaskets because of their excellent leak tightness and nonhazardous physical degradation properties. The research focuses profoundly on the adverse influence of temperature and thermal cycles on the creep and cumulative damage phenomenon under compressive load. Virgin and expanded PolyTetraFluoroEthylene (PTFE) are tested under 28 and 41 MPa of gasket stress at different temperatures. Intricate analysis of creep under coalesces of thermal ratcheting and principal stress is achieved through Universal Gasket Rig (UGR). The instigated cumulative damage is distinguishable into upper and lower bound temperature region indicating the escalation and decrease of thickness change during cycling which saturates after 12 thermal cycles for expanded PTFE while no saturation is reached for virgin PTFE in even after 20 thermal cycles. Percentage of thickness reduction at different applied stress is nearly the same for virgin PTFE whereas expanded PTFE shows largest reduction under lower stress. Compressive creep bespeaks the impact of temperature and load, thereby dictating the magnitude of ratcheting damage and contrariwise. Finally, the creep and thermal ratcheting has a proliferating effect on value of the coefficient of thermal expansion for all chosen gaskets. Copyright © 2017 VBRI Press.

Transport and Diffusion Enhancement in Experimentally Realized Non-Gaussian Correlated Ratchets.

Living cells are known to generate non-Gaussian active fluctuations significantly larger than thermal fluctuations owing to various active processes. Understanding the effect of these active fluctuations on various physicochemical processes, such as the transport of molecular motors, is a fundamental problem in nonequilibrium physics. Therefore, we experimentally and numerically studied an active Brownian ratchet comprising a colloidal particle in an optically generated asymmetric periodic potential driven by non-Gaussian noise having finite-amplitude active bursts, each arriving at random and decaying exponentially. We find that the particle velocity is maximum for relatively sparse bursts with finite correlation time and non-Gaussian distribution. These occasional kicks, which produce Brownian yet non-Gaussian diffusion, are more efficient for transport and diffusion enhancement of the particle than the incessant kicks of active Ornstein-Uhlenbeck noise.

Operating Characteristics of Metal Hydride-Based Solar Energy Storage Systems

Thermochemical energy storage systems, based on a high-temperature metal hydride coupled with a low-temperature metal hydride, represent a valid option to store thermal energy for concentrating solar power plant applications. The operating characteristics are investigated for a tandem hydride bed energy storage system, using a transient lumped parameter model developed to identify the technical performance of the proposed system. The results show that, without operational control, the system undergoes a thermal ratcheting process, causing the metal hydride concentrations to accumulate hydrogen in the high-temperature bed over time, and deplete hydrogen in the low temperature. This unbalanced system is compared with a ’thermally balanced’ system, where the thermal ratcheting is mitigated by thermally balancing the overall system. The analysis indicates that thermally balanced systems stabilize after the first few cycles and remain so for long-term operation, demonstrating their potential for practical thermal energy storage system applications.

Structural basis for antibody binding to adenylate cyclase toxin reveals RTX linkers as neutralization-sensitive epitopes.

RTX leukotoxins are a diverse family of prokaryotic virulence factors that are secreted by the type 1 secretion system (T1SS) and target leukocytes to subvert host defenses. T1SS substrates all contain a C-terminal RTX domain that mediates recruitment to the T1SS and drives secretion via a Brownian ratchet mechanism. Neutralizing antibodies against the Bordetella pertussis adenylate cyclase toxin, an RTX leukotoxin essential for B. pertussis colonization, have been shown to target the RTX domain and prevent binding to the αMβ2 integrin receptor. Knowledge of the mechanisms by which antibodies bind and neutralize RTX leukotoxins is required to inform structure-based design of bacterial vaccines, however, no structural data are available for antibody binding to any T1SS substrate. Here, we determine the crystal structure of an engineered RTX domain fragment containing the αMβ2-binding site bound to two neutralizing antibodies. Notably, the receptor-blocking antibodies bind to the linker regions of RTX blocks I–III, suggesting they are key neutralization-sensitive sites within the RTX domain and are likely involved in binding the αMβ2 receptor. As the engineered RTX fragment contained these key epitopes, we assessed its immunogenicity in mice and showed that it elicits similar neutralizing antibody titers to the full RTX domain. The results from these studies will support the development of bacterial vaccines targeting RTX leukotoxins, as well as next-generation B. pertussis vaccines.

Model Simulation of Creep and Thermal Ratcheting of Engineering Polymers

AbstractIn the present work, the creep response at specific temperatures and stress level of several polymers has been modeled by a viscoelastic model, analyzed in previous works. In particular, the experimental creep results under thermal cycling of polymers used in bolted flange connections, utilized as components of pressure vessel and piping are employed. The analysis is focused on the experimental results for polymeric flange materials like high density polyethylene and three types of gasket materials, namely poly‐tetrafluoroethylene PTFE (expanded e‐ and virgin v‐) and clickable nucleic acid. It has been proved that by the implementation of the model on a simple creep curve at a specific temperature, the model parameters could be evaluated. Hereafter, by imposing a thermal cycling process, two more parameters, associated with thermal ratcheting, could be acquired. It is found that the thermal ratcheting behavior exhibited by the employed materials, could be captured with a good accuracy. Given that the effect of thermal ratcheting on the long‐time performance of polymers in targeted applications is a crucial issue, the research findings in the present work are encouraging for the design of appropriate materials, and the prediction of thermal ratcheting.

Spatial control over near-critical-point operation ensures fidelity of ParABS-mediated DNA partition

In bacteria, most low-copy-number plasmid and chromosomally encoded partition systems belong to the tripartite ParABS partition machinery. Despite the importance in genetic inheritance, the mechanisms of ParABS-mediated genome partition are not well understood. Combining theory and experiment, we provided evidence that the ParABS system—DNA partitioning in vivo via the ParA-gradient-based Brownian ratcheting—operates near a transition point in parameter space (i.e., a critical point), across which the system displays qualitatively different motile behaviors. This near-critical-point operation adapts the segregation distance of replicated plasmids to the half length of the elongating nucleoid, ensuring both cell halves to inherit one copy of the plasmids. Further, we demonstrated that the plasmid localizes the cytoplasmic ParA to buffer the partition fidelity against the large cell-to-cell fluctuations in ParA level. The spatial control over the near-critical-point operation not only ensures both sensitive adaptation and robust execution of partitioning but also sheds light on the fundamental question in cell biology: how do cells faithfully measure cellular-scale distance by only using molecular-scale interactions?

The nucleotide addition cycle of the SARS-CoV-2 polymerase.

Coronaviruses have evolved elaborate multisubunit machines to replicate and transcribe their genomes. Central to these machines are the RNA-dependent RNA polymerase subunit (nsp12) and its intimately associated cofactors (nsp7 and nsp8). We use a high-throughput magnetic-tweezers approach to develop a mechanochemical description of this core polymerase. The core polymerase exists in at least three catalytically distinct conformations, one being kinetically consistent with incorporation of incorrect nucleotides. We provide evidence that the RNA-dependent RNA polymerase (RdRp) uses a thermal ratchet instead of a power stroke to transition from the pre- to post-translocated state. Ultra-stable magnetic tweezers enable the direct observation of coronavirus polymerase deep and long-lived backtracking that is strongly stimulated by secondary structures in the template. The framework we present here elucidates one of the most important structure-dynamics-function relationships in human health today and will form the grounds for understanding the regulation of this complex.

Alexander Spirin’s Vision of the Ribosome as a Thermal Ratchet Machine

Alexander Spirin’s Vision of the Ribosome as a Thermal Ratchet Machine

A Brownian ratchet model for DNA loop extrusion by the cohesin complex.

The cohesin complex topologically encircles DNA to promote sister chromatid cohesion. Alternatively, cohesin extrudes DNA loops, thought to reflect chromatin domain formation. Here, we propose a structure-based model explaining both activities. ATP and DNA binding promote cohesin conformational changes that guide DNA through a kleisin N-gate into a DNA gripping state. Two HEAT-repeat DNA binding modules, associated with cohesin's heads and hinge, are now juxtaposed. Gripping state disassembly, following ATP hydrolysis, triggers unidirectional hinge module movement, which completes topological DNA entry by directing DNA through the ATPase head gate. If head gate passage fails, hinge module motion creates a Brownian ratchet that, instead, drives loop extrusion. Molecular-mechanical simulations of gripping state formation and resolution cycles recapitulate experimentally observed DNA loop extrusion characteristics. Our model extends to asymmetric and symmetric loop extrusion, as well as z-loop formation. Loop extrusion by biased Brownian motion has important implications for chromosomal cohesin function.

How Influenza’s Spike Motor Works

While often believed to be a passive agent that merely exploits its host's metabolism, the influenza virus has recently been shown to actively move across glycan-coated surfaces. This form of enzymatically driven surface motility is currently not well understood and has been loosely linked to burnt-bridge Brownian ratchet mechanisms. Starting from known properties of influenza's spike proteins, we develop a physical model that quantitatively describes the observed motility. It predicts a collectively emerging dynamics of spike proteins and surface-bound ligands that combined with the virus' geometry give rise to a self-organized rolling propulsion. We show that in contrast to a Brownian ratchet, the rotary spike drive is not fluctuation driven but operates optimally as a macroscopic engine in the deterministic regime. The mechanism also applies to relatives of influenza and to man-made analogs like DNA monowheels and should give guidelines for their optimization.

Experimental demonstration of optical Brownian ratchet by controllable phase profile of light

Brownian ratchet has emerged as a promising tool for deeply understanding motion mechanism of molecules and proteins, and dynamically manipulating particles in non-equilibrium thermodynamics state. Here, we propose and experimentally demonstrate a new type of optical Brownian ratchet, as generated by controllable phase profiles in holographic optical trapping system. The potential energy profiles are dynamically switched in on-off mode, by using Labview software. Experimental results show that not only high speed but also large step distance can be easily achieved in Brownian ratchet, in which the average velocity of forward motion is around 28 μm/s and step distance is about 42 μm. Importantly, the velocity, step distance and motion path can be easily adjusted by manipulating the holograms, which exhibit high flexibility, easy control and excellent capability. This study provides a new way to explore non-equilibrium dynamics at the nanoscale level, and create novel functions in nanoparticle manipulation.