SEARCH · Searcharxiv

Results for “physics.bio-ph”

Search indexed arXiv papers on artificial intelligence, large language models, computer vision and robotics. Read source abstracts and follow links to arXiv.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 487 records · Page 27Linked to original sources

arXiv2014

Characterization of the low temperature properties of a simplified protein model

Prompted by results that showed that a simple protein model, the frustrated Gō model, appears to exhibit a transition reminiscent of the protein dynamical transition, we examine the validity of this model to describe the low-temperature properties of proteins. First, we examine equilibrium fluctuations. We calculate its incoherent neutron-scattering structure factor and show that it can be well described by a theory using the one-phonon approximation. By performing an inherent structure analysis, we assess the transitions among energy states at low temperatures. Then, we examine non-equilibrium fluctuations after a sudden cooling of the protein. We investigate the violation of the fluctuation--dissipation theorem in order to analyze the protein glass transition. We find that the effective temperature of the quenched protein deviates from the temperature of the thermostat, however it relaxes towards the actual temperature with an Arrhenius behavior as the waiting time increases. These results of the equilibrium and non-equilibrium studies converge to the conclusion that the apparent dynamical transition of this coarse-grained model cannot be attributed to a glassy behavior.

cond-mat.stat-mech↗

arXiv2014

Self-Organized Vortices of Circling Self-Propelled Particles and Curved Active Flagella

Self-propelled point-like particles move along circular trajectories when their translocation velocity is constant and the angular velocity related to their orientation vector is also constant. We investigate the collective behavior of ensembles of such circle swimmers by Brownian dynamics simulations. If the particles interact via a "velocity-trajectory coordination" rule within neighboring particles, a self-organized vortex pattern emerges. This vortex pattern is characterized by its particle-density correlation function $G_ρ$, the density correlation function $G_c$ of trajectory centers, and an order parameter $S$ representing the degree of the aggregation of the particles. Here, we systematically vary the system parameters, such as the particle density and the interaction range, in order to reveal the transition of the system from a light-vortex-dominated to heavy-vortex-dominated state, where vortices contain mainly a single and many self-propelled particles, respectively. We also study a semi-dilute solution of curved, sinusoidal-beating flagella, as an example of circling self-propelled particles with explicit propulsion mechanism and excluded-volume interactions. Our simulation results are compared with previous experimental results for the vortices in sea-urchin sperm solutions near a wall. The properties of the vortices in simulations and experiments are found to agree quantitatively.

physics.bio-ph↗

arXiv2011

Output-input coupling in thermally fluctuating biomolecular machines

Biological molecular machines are proteins that operate under isothermal conditions hence are referred to as free energy transducers. They can be formally considered as enzymes that simultaneously catalyze two chemical reactions: the free energy-donating reaction and the free energy-accepting one. Most if not all biologically active proteins display a slow stochastic dynamics of transitions between a variety of conformational substates composing their native state. In the steady state, this dynamics is characterized by mean first-passage times between transition substates of the catalyzed reactions. On taking advantage of the assumption that each reaction proceeds through a single pair (the gate) of conformational transition substates of the enzyme-substrates complex, analytical formulas were derived for the flux-force dependence of the both reactions, the respective stalling forces and the degree of coupling between the free energy-accepting (output) reaction flux and the free energy-donating (input) one. The theory is confronted with the results of random walk simulations on the 5-dimensional hypercube. The formal proof is given that in the case of reactions proceeding through single gates, the degree of coupling cannot exceed unity. As some experiments suggest such exceeding, looking for conditions of increasing the degree of coupling over unity challenges theory. Though no analytical formulas for models involving more transition substates are available, study simulations of random walks on several model networks indicate that the case of the degree of coupling value higher than one occurs in a natural way for scale-free tree-like networks. This supports a hypothesis that the protein conformational transition networks, like higher level biological networks: the proteome and the metabolome, have evolved in a process of self-organized criticality.

physics.bio-ph↗

arXiv2014

Efficient fold-change detection based on protein-protein interactions

Various biological sensory systems exhibit a response to a relative change of the stimulus, often referred to as fold-change detection. In the last few years fold-change detecting mechanisms, based on transcriptional networks, have been proposed. Here we present fold-change detecting mechanism, based on protein-protein interactions, consisting of two interacting proteins. This mechanism, in contrast to previously proposed mechanisms, does not consume chemical energy and is not subject to transcriptional and translational noise. We show by analytical and numerical calculations, that the mechanism can have a fast, precise and efficient response for parameters that are relevant to eukaryotic cells.

physics.bio-ph↗

arXiv2014

Avian photoreceptor patterns represent a disordered hyperuniform solution to a multiscale packing problem

Optimal spatial sampling of light rigorously requires that identical photoreceptors be arranged in perfectly regular arrays in two dimensions. Examples of such perfect arrays in nature include the compound eyes of insects and the nearly crystalline photoreceptor patterns of some fish and reptiles. Birds are highly visual animals with five different cone photoreceptor subtypes, yet their photoreceptor patterns are not perfectly regular. By analyzing the chicken cone photoreceptor system consisting of five different cell types using a variety of sensitive microstructural descriptors, we find that the disordered photoreceptor patterns are ``hyperuniform'' (exhibiting vanishing infinite-wavelength density fluctuations), a property that had heretofore been identified in a unique subset of physical systems, but had never been observed in any living organism. Remarkably, the photoreceptor patterns of both the total population and the individual cell types are simultaneously hyperuniform. We term such patterns ``multi-hyperuniform'' because multiple distinct subsets of the overall point pattern are themselves hyperuniform. We have devised a unique multiscale cell packing model in two dimensions that suggests that photoreceptor types interact with both short- and long-ranged repulsive forces and that the resultant competition between the types gives rise to the aforementioned singular spatial features characterizing the system, including multi-hyperuniformity.

cond-mat.stat-mech↗

arXiv2013

Rare-event trajectory ensemble analysis reveals metastable dynamical phases in lattice proteins

We explore the dynamical large-deviations of a lattice heteropolymer model of a protein by means of path sampling of trajectories. We uncover the existence of non-equilibrium dynamical phase-transitions in ensembles of trajectories between active and inactive dynamical phases, whose nature depends on properties of the interaction potential. When the full heterogeneity of interactions due to the amino-acid sequence is preserved, as in a fully interacting model or in a heterogeneous version of the Gō model where only native interactions are considered, the transition is between the equilibrium native state and a highly native but kinetically trapped state. In contrast, for the homogeneous Gō model, where there is a single native energy and the sequence plays no role, the dynamical transition is a direct consequence of the static bi-stability between unfolded and native states. In the heterogeneous case the native-active and native-inactive states, despite their static similarity, have widely varying dynamical properties, and the transition between them occurs even in lattice proteins whose sequences are designed to make them optimal folders.

cond-mat.soft↗

arXiv2014

Role of functionality in two-component signal transduction: A stochastic study

We present a stochastic formalism for signal transduction processes in bacterial two-component system. Using elementary mass action kinetics, the proposed model takes care of signal transduction in terms of phosphotransfer mechanism between the cognate partners of a two-component system, viz, the sensor kinase and the response regulator. Based on the difference in functionality of the sensor kinase, the noisy phosphotransfer mechanism has been studied for monofunctional and bifunctional two component system using the formalism of linear noise approximation. Steady state analysis of both models quantifies different physically realizable quantities, e.g., variance, coefficient of variation, mutual information. The resultant data reveals that both systems reliably transfer information of extra-cellular environment under low external stimulus and at high kinase and phosphatase regime. We extend our analysis further by studying the role of two-component system in downstream gene regulation.

q-bio.SC↗

arXiv2014

Optimal search in interacting populations:Gaussian jumps vs Levy flights

We investigated the relationships between search efficiency, movement strategy, and non-local communication in the biological context of animal foraging. We considered situations where the members of a population of foragers perform either Gaussian jumps or Levy flights, and show that the search time is minimized when communication among individuals occurs at intermediate ranges, independently of the type of movement. Additionally, while Brownian strategies are more strongly influenced by the communication mechanism, Levy flights still result in shorter overall search durations.

cond-mat.stat-mech↗

arXiv2014

Interfaces with internal structures in generalized rock-paper-scissors models

In this work we investigate the development of stable dynamical structures along interfaces separating domains belonging to enemy partnerships, in the context of cyclic predator-prey models with an even number of species $N \ge 8$. We use both stochastic and field theory simulations in one and two spatial dimensions, as well as analytical arguments, to describe the association at the interfaces of mutually neutral individuals belonging to enemy partnerships and to probe their role in the development of the dynamical structures at the interfaces. We identify an interesting behaviour associated to the symmetric or asymmetric evolution of the interface profiles depending on whether $N/2$ is odd or even, respectively. We also show that the macroscopic evolution of the interface network is not very sensitive internal structure of the interfaces. Although this work focus on cyclic predator prey-models with an even number of species, we argue that the results are expected to be quite generic in the context of spatial stochastic May-Leonard models.

physics.bio-ph↗

arXiv2014

Dynamics of polymer ejection from capsid

Polymer ejection from a capsid through a nanoscale pore is an important biological process with relevance to modern biotechnology. Here, we study generic capsid ejection using Langevin dynamics. We show that even when the ejection takes place within the drift-dominated region there is a very high probability for the ejection process not to be completed. Introducing a small aligning force at the pore entrance enhances ejection dramatically. Such a pore asymmetry is a candidate for a mechanism by which a viral ejection is completed. By detailed high-resolution simulations we show that such capsid ejection is an out-of-equilibrium process that shares many common features with the much studied driven polymer translocation through a pore in a wall or a membrane. We find that the escape times scale with polymer length, $τ\sim N^α$. We show that for the pore without the asymmetry the previous predictions corroborated by Monte Carlo simulations do not hold. For the pore with the asymmetry the scaling exponent varies with the initial monomer density (monomers per capsid volume) $ρ$ inside the capsid. For very low densities $ρ\le 0.002$ the polymer is only weakly confined by the capsid, and we measure $α= 1.33$, which is close to $α= 1.4$ obtained for polymer translocation. At intermediate densities the scaling exponents $α= 1.25$ and $1.21$ for $ρ= 0.01$ and $0.02$, respectively. These scalings are in accord with a crude derivation for the lower limit $α= 1.2$. For the asymmetrical pore precise scaling breaks down, when the density exceeds the value for complete confinement by the capsid, $ρ\gtrapprox 0.25$. The high-resolution data show that the capsid ejection for both pores, analogously to polymer translocation, can be characterized as a multiplicative stochastic process that is dominated by small-scale transitions.

physics.bio-ph↗

arXiv2014

Geometry for a `penguin-albatross' rookery

We introduce a simple ecological model describing the spatial organization of two interacting populations whose individuals are indifferent to conspecifics and avoid the proximity to heterospecifics. At small population densities $Φ$ a non-trivial structure is observed where clusters of individuals arrange into a rhomboidal bipartite network with an average degree of four. For $Φ\rightarrow0$ the length scale, order parameter and susceptibility of the network exhibit power-law divergences compatible with hyper-scaling, suggesting the existence of a zero density - non-trivial - critical point. At larger densities a critical threshold $Φ_{c}$ is identified above which the evolution toward a partially ordered configuration is prevented and the system becomes jammed in a fully mixed state.

q-bio.PE↗

arXiv2014

Initiation and blocking of the action potential in the axon in weak ultrasonic or microwave fields

In this paper, we analyze the effect of the redistribution of the transmembrane ion channels in the axon caused by longitudinal acoustic vibrations of the membrane. These oscillations can be excited by an external source of ultrasound and weak microwave radiation interacting with the charges sitting on the surface of the lipid membrane. It is shown, using the Hodgkin-Huxley model of the axon, that the density redistribution of transmembrane sodium channels may reduce the threshold of the action potential, up to its spontaneous initiation. At the significant redistribution of sodium channels in membrane, the rarefaction zones of the transmembrane channels density are formed, blocking the propagation of the action potential. Blocking the action potential propagation along the axon is shown to cause anestesia in the example case of a squid axon. Various approaches to experimental observation of the effects considered in this paper are discussed.

physics.bio-ph↗

arXiv2014

Suppression and enhancement of transcriptional noise by DNA looping

DNA looping has been observed to enhance and suppress transcriptional noise but it is uncertain which of these two opposite effects is to be expected for given conditions. Here, we derive analytical expressions for the main quantifiers of transcriptional noise in terms of the molecular parameters and elucidate the role of DNA looping. Our results rationalize paradoxical experimental observations and provide the first quantitative explanation of landmark individual-cell measurements at the single molecule level on the classical lac operon genetic system [Choi et al., Science 322, 442-446 (2008)].

q-bio.SC↗

arXiv2014

Relaxation and curvature-induced molecular flows within multicomponent membranes

The quantitative understanding of membranes is still rooted in work performed in the 1970s by Helfrich and others, concerning amphiphilic bilayers. However, most biological membranes contain a wide variety of nonamphiphilic molecules too. Drawing analogy with the physics of nematic/non-nematic mixtures, we present a dynamical (out of equilibrium) description of such multicomponent membranes. The approach combines nematohydrodynamics in the linear regime and a proper use of (differential) geometry. The main result is to demonstrate that one can obtain equations describing a cross-diffusion effect (similar to the Soret and Dufour effects) between curvature and the (in-membrane) flow of amphiphilic molecules relative to nonamphiphilic ones. Surprisingly, the shape of a membrane relaxes according to a simple heat equation in the mean curvature, a process that is accompanied by a simultaneous boost to the diffusion of amphiphiles away from regions of high curvature. The model also predicts the inverse process, by which the forced bending of a membrane induces a flow of amphiphilic molecules towards areas of high curvature. In principle, numerical values for the relevant diffusion coefficients should be verifiable by experiment.

cond-mat.soft↗

arXiv2014

Velocity alignment leads to high persistence in confined cells

Many cell types display random motility on two-dimensional substrates, but crawl persistently in a single direction when confined in a microchannel or on an adhesive micropattern. Does this imply that the motility mechanism of confined cells is fundamentally different from that of unconfined cells? We argue that both free- and confined- cell migration may be described by a generic model of cells as "velocity aligning" active Brownian particles previously proposed to solve a completely separate problem in collective cell migration. Our model can be mapped to a diffusive escape over a barrier and analytically solved to determine the cell's orientation distribution and repolarization rate. In quasi-one-dimensional confinement, velocity-aligning cells maintain their direction for times that can be exponentially larger than their persistence time in the absence of confinement. Our results suggest an important new connection between single- and collective- cell migration: high persistence in confined cells corresponds with fast alignment of velocity to cell-cell forces.

physics.bio-ph↗

arXiv2017

A statistical analysis of particle trajectories in living cells

Recent advances in molecular biology and fluorescence microscopy imaging have made possible the inference of the dynamics of single molecules in living cells. Such inference allows to determine the organization and function of the cell. The trajectories of particles in the cells, computed with tracking algorithms, can be modelled with diffusion processes. Three types of diffusion are considered : (i) free diffusion; (ii) subdiffusion or (iii) superdiffusion. The Mean Square Displacement (MSD) is generally used to determine the different types of dynamics of the particles in living cells (Qian, Sheetz and Elson 1991). We propose here a non-parametric three-decision test as an alternative to the MSD method. The rejection of the null hypothesis -- free diffusion -- is accompanied by claims of the direction of the alternative (subdiffusion or a superdiffusion). We study the asymptotic behaviour of the test statistic under the null hypothesis, and under parametric alternatives which are currently considered in the biophysics literature, (Monnier et al,2012) for example. In addition, we adapt the procedure of Benjamini and Hochberg (2000) to fit with the three-decision test setting, in order to apply the test procedure to a collection of independent trajectories. The performance of our procedure is much better than the MSD method as confirmed by Monte Carlo experiments. The method is demonstrated on real data sets corresponding to protein dynamics observed in fluorescence microscopy.

stat.AP↗

arXiv2018

Thermodynamics of Evolutionary Games

How cooperation can evolve between players is an unsolved problem of biology. Here we use Hamiltonian dynamics of models of the Ising type to describe populations of cooperating and defecting players to show that the equilibrium fraction of cooperators is given by the expectation value of a thermal observable akin to a magnetization. We apply the formalism to the Public Goods game with three players, and show that a phase transition between cooperation and defection occurs that is equivalent to a transition in one-dimensional Ising crystals with long-range interactions. We then investigate the effect of punishment on cooperation and find that punishment plays the role of a magnetic field that leads to an "alignment" between players, thus encouraging cooperation. We suggest that a thermal Hamiltonian picture of the evolution of cooperation can generate other insights about the dynamics of evolving groups by mining the rich literature of critical dynamics in low-dimensional spin systems.

q-bio.PE↗

arXiv2018

Topological Bounds of Bending Energy for Lipid Vesicles

The Helfrich bending energy plays an important role in providing a mechanism for the conformation of a lipid vesicle in theoretical biophysics, which is governed by the principle of energy minimization over configurations of appropriate topological characteristics. We will show that the presence of a quantity called the spontaneous curvature obstructs the existence of a minimizer of the Helfrich energy over the set of embedded ring tori. Besides, despite the well-realized knowledge that lipid vesicles may present themselves in a variety of shapes of complicated topology, there is a lack of topological bounds for the Helfrich energy. To overcome these difficulties, we consider a general scale-invariant anisotropic curvature energy that extends the Canham elastic bending energy developed in modeling a biconcave-shaped red blood cell. We will show that, up to a rescaling of the generating radii, there is a unique minimizer of the energy over the set of embedded ring tori, in the entire parameter regime, which recovers the Willmore minimizer in its Canham isotropic limit. We also show how elevated anisotropy favors energetically a clear transition from spherical-, to ellipsoidal-, and then to biconcave-shaped surfaces, for a lipid vesicle. We then establish some genus-dependent topological lower and upper bounds for the anisotropic energy. Finally, we derive the shape equation of the generalized bending energy, which extends the well-known Helfrich shape equation.

cond-mat.soft↗