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At least 649 records · Page 36Linked to original sources
arXiv2003

When translocation dynamics becomes anomalous

Recent single molecule experiments probing the passage process of a short single-stranded DNA (ssDNA) through a membrane channel (translocation) allow to measure the passage time distribution. Building on a recent modelling approach (D. K. Lubensky and D. R. Nelson, Biophys. J. 77, 1824 (1999)), which has been demonstrated to be valid for chains of up to $\simeq 300$ nucleotides and therefore well applies to the system we have in mind, we discuss the consequences if the associated dynamics is not of Markov origin, but if strong memory effects prevail during the translocation. Motivation is drawn from recent results indicating that the distribution of translocation times is broader than predicted by simple Markovian models based on Brownian motion.

cond-mat.stat-mech↗
arXiv2003

Protein Evolution within a Structural Space

Understanding of the evolutionary origins of protein structures represents a key component of the understanding of molecular evolution as a whole. Here we seek to elucidate how the features of an underlying protein structural "space" might impact protein structural evolution. We approach this question using lattice polymers as a completely characterized model of this space. We develop a measure of structural comparison of lattice structures that is analgous to the one used to understand structural similarities between real proteins. We use this measure of structural relatedness to create a graph of lattice structures and compare this graph (in which nodes are lattice structures and edges are defined using structural similarity) to the graph obtained for real protein structures. We find that the graph obtained from all compact lattice structures exhibits a distribution of structural neighbors per node consistent with a random graph. We also find that subgraphs of 3500 nodes chosen either at random or according to physical constraints also represent random graphs. We develop a divergent evolution model based on the lattice space which produces graphs that, within certain parameter regimes, recapitulate the scale-free behavior observed in similar graphs of real protein structures.

cond-mat.soft↗
arXiv2003

Modeling extracellular field potentials and the frequency-filtering properties of extracellular space

Extracellular local field potentials (LFP) are usually modeled as arising from a set of current sources embedded in a homogeneous extracellular medium. Although this formalism can successfully model several properties of LFPs, it does not account for their frequency-dependent attenuation with distance, a property essential to correctly model extracellular spikes. Here we derive expressions for the extracellular potential that include this frequency-dependent attenuation. We first show that, if the extracellular conductivity is non-homogeneous, there is induction of non-homogeneous charge densities which may result in a low-pass filter. We next derive a simplified model consisting of a punctual (or spherical) current source with spherically-symmetric conductivity/permittivity gradients around the source. We analyze the effect of different radial profiles of conductivity and permittivity on the frequency-filtering behavior of this model. We show that this simple model generally displays low-pass filtering behavior, in which fast electrical events (such as Na$^+$-mediated action potentials) attenuate very steeply with distance, while slower (K$^+$-mediated) events propagate over larger distances in extracellular space, in qualitative agreement with experimental observations. This simple model can be used to obtain frequency-dependent extracellular field potentials without taking into account explicitly the complex folding of extracellular space.

physics.bio-ph↗
arXiv1997

Dynamically-Stabilized Pores in Bilayer Membranes

Zhelev and Needham have recently created large, quasi-stable pores in artificial lipid bilayer vesicles [Biochim. Biophys. Acta 1147 (1993) 89]. Initially created by electroporation, the pores remain open for up to several seconds before quickly snapping shut. This result is surprising in light of the large line tension for holes in bilayer membranes and the rapid time scale for closure of large pores. We show how pores can be dynamically stabilized via a new feedback mechanism. We also explain quantitatively the observed sudden pore closure as a tangent bifurcation. Finally we show how Zhelev and Needham's experiment can be used to measure accurately the pore line tension, an important material parameter. For their SOPC/CHOL mixture we obtain a line tension of 2.6 10^{-6} erg/cm.

cond-mat.soft↗
arXiv1999

Unbinding of Retinoic Acid from its Receptor Studied by Steered Molecular Dynamics

Retinoic acid receptor (RAR) is a ligand-dependent transcription factor that regulates the expression of genes involved in cell growth, differentiation, and development. Binding of the retinoic acid hormone to RAR is accompanied by conformational changes in the protein which induce transactivation or transrepression of the target genes. In this paper we present a study of the hormone binding/unbinding process in order to clarify the role of some of the amino acid contacts and identify possible pathways of the all-trans retinoic acid binding/unbinding to/from human retinoic acid receptor (hRAR)-g. Three possible pathways were explored using steered molecular dynamics simulations. Unbinding was induced on a time scale of 1 ns by applying external forces to the hormone. The simulations suggest that the hormone may employ one pathway for binding and an alternative "back door" pathway for unbinding.

physics.bio-ph↗
arXiv2000

Replica-exchange multicanonical algorithm and multicanonical replica-exchange method for simulating systems with rough energy landscape

We propose two efficient algorithms for configurational sampling of systems with rough energy landscape. The first one is a new method for the determination of the multicanonical weight factor. In this method a short replica-exchange simulation is performed and the multicanonical weight factor is obtained by the multiple-histogram reweighting techniques. The second one is a further extension of the first in which a replica-exchange multicanonical simulation is performed with a small number of replicas. These new algorithms are particularly useful for studying the protein folding problem.

cond-mat.stat-mech↗
arXiv1997

Parallel Tempering Algorithm for Conformational Studies of Biological Molecules

The effectiveness of a new algorithm, parallel tempering, is studied for numerical simulations of biological molecules. These molecules suffer from a rough energy landscape. The resulting slowing down in numerical simulations is overcome by the new method. This is demonstrated by performing simulations with high statistics for one of the simplest peptides, Met-enkephalin. The numerical effectiveness of the new technique was found to be much better than traditional methods and is comparable to sophisticated methods like generalized ensemble techniques.

physics.chem-ph↗
arXiv1998

Stochastic dynamics simulations in a new generalized ensemble

We develop a formulation for molecular dynamics, Langevin, and hybrid Monte Carlo algorithms in the recently proposed generalized ensemble that is based on a physically motivated realisation of Tsallis weights. The effectiveness of the methods are tested with an energy function for a protein system. Simulations in this generalized ensemble by the three methods are performed for a penta peptide, Met-enkephalin. For each algorithm, it is shown that from only one simulation run one can not only find the global-minimum-energy conformation but also obtain probability distributions in canonical ensemble at any temperature, which allows the calculation of any thermodynamic quantity as a function of temperature.

physics.bio-ph↗
arXiv2002

Folding in lattice models with side chains

The folding kinetics of three-dimensional lattice Go models with side chains is studied using two different Monte Carlo move sets. A flexible move set based on single, double and triple backbone moves is found to be far superior compared to the standard Monte Carlo dynamics. It was found that the folding time grows as a power law with the chain length and the corresponding exponent $λ\approx 3.6$ for Go models. The study shows that the incorporation of side chains dramatically slows down folding rates.

cond-mat.soft↗
arXiv2001

Generalized-ensemble simulations of spin systems and protein systems

In complex systems such as spin systems and protein systems, conventional simulations in the canonical ensemble will get trapped in states of energy local minima. We employ the generalized-ensemble algorithms in order to overcome this multiple-minima problem. Three well-known generalized-ensemble algorithms, namely, multicanonical algorithm, simulated tempering, and replica-exchange method, are described. We then present three new generalized-ensemble algorithms based on the combinations of the three methods. Effectiveness of the new methods are tested with a Potts model and protein systems.

cond-mat.stat-mech↗
arXiv2002

A new dimension to Turing patterns

It is well known that simple reaction-diffusion systems can display very rich pattern formation behavior. Here we have studied two examples of such systems in three dimensions. First we investigate the morphology and stability of a generic Turing system in three dimensions and then the well-known Gray-Scott model. In the latter case, we added a small number of morphogen sources in the system in order to study its robustness and the formation of connections between the sources. Our results raise the question of whether Turing patterning can produce an inductive signaling mechanism for neuronal growth.

cond-mat.stat-mech↗
arXiv2002

Behavior of tumors under nonstationary theraphy

We present a model for the interaction dynamics of lymphocytes-tumor cells population. This model reproduces all known states for the tumor. Futherly,we develop it taking into account periodical immunotheraphy treatment with cytokines alone. A detailed analysis for the evolution of tumor cells as a function of frecuency and theraphy burden applied for the periodical treatment is carried out. Certain threshold values for the frecuency and applied doses are derived from this analysis. So it seems possible to control and reduce the growth of the tumor. Also, constant values for cytokines doses seems to be a succesful treatment.

math-ph↗
arXiv1997

The Modular Structure of Kauffman Networks

This is the second paper of a series of two about the structural properties that influence the asymptotic dynamics of Random Boolean Networks. Here we study the functionally independent clusters in which the relevant elements, introduced and studied in our first paper, are subdivided. We show that the phase transition in Random Boolean Networks can also be described as a percolation transition. The statistical properties of the clusters of relevant elements (that we call modules) give an insight on the scaling behavior of the attractors of the critical networks that, according to Kauffman, have a biological analogy as a model of genetic regulatory systems.

cond-mat.dis-nn↗
arXiv1999

A Robust Method for Detecting Interdependences: Application to Intracranially Recorded EEG

We present a measure for characterizing statistical relationships between two time sequences. In contrast to commonly used measures like cross-correlations, coherence and mutual information, the proposed measure is non-symmetric and provides information about the direction of interdependence. It is closely related to recent attempts to detect generalized synchronization. However, we do not assume a strict functional relationship between the two time sequences and try to define the measure so as to be robust against noise, and to detect also weak interdependences. We apply our measure to intracranially recorded electroencephalograms of patients suffering from severe epilepsies.

chao-dyn↗
arXiv2001

A Sucrose Solution Application to the Study of Model Biological Membranes

The small-angle X-ray and neutron scattering, time resolved X-ray small-angle and wide-angle diffraction coupled with differential scanning calorimetry have been applied to the investigation of unilamellar and multilamellar dimyristoylphosphatidylcholine (DMPC) vesicles in sucrose buffers with sucrose concentrations from 0 to 60%. Sucrose buffer decreased vesicle size and polydispersity and increased an X-ray contrast between phospholipid membrane and bulk solvent sufficiently. No influence of sucrose on the membrane thickness or mutual packing of hydrocarbon chains has been detected. The region of sucrose concentrations 30%-40% created the best experimental conditions for X-ray small-angle experiments with phospholipid vesicles.

physics.bio-ph↗
arXiv2002

Anomalous relaxation kinetics of biological lattice-ligand binding models

We discuss theoretical models for the cooperative binding dynamics of ligands to substrates, such as dimeric motor proteins to microtubules or more extended macromolecules like tropomyosin to actin filaments. We study the effects of steric constraints, size of ligands, binding rates and interaction between neighboring proteins on the binding dynamics and binding stoichiometry. Starting from an empty lattice the binding dynamics goes, quite generally, through several stages. The first stage represents fast initial binding closely resembling the physics of random sequential adsorption processes. Typically this initial process leaves the system in a metastable locked state with many small gaps between blocks of bound molecules. In a second stage the gaps annihilate slowly as the ligands detach and reattach. This results in an algebraic decay of the gap concentration and interesting scaling behavior. Upon identifying the gaps with particles we show that the dynamics in this regime can be explained by mapping it onto various reaction-diffusion models. The final approach to equilibrium shows some interesting dynamic scaling properties. We also discuss the effect of cooperativity on the equilibrium stoichiometry, and their consequences for the interpretation of biochemical and image reconstruction results.

cond-mat.soft↗
arXiv2002

A Diffusion-Based Approach to Geminate Recombination of Heme Proteins with Small Ligands

A model of postphotodissociative monomolecular (geminate) recombination of heme proteins with small ligands (NO, O2 or CO) is represented. The non-exponential decay with time for the probability to find a heme in unbound state is interpreted in terms of diffusion-like migration of ligabs physics/0212040 and between protein cavities. The temporal behavior for the probability is obtained from numerical simulation and specified by two parameters: the time τ_{reb} of heme-ligand rebinding for the ligand localized inside the heme pocket and the time τ_{esc} of ligand escape from the pocket. The model is applied in the analysis of available experimental data for geminate reoxygenation of human hemoglobin HbA. Our simulation is in good agreement with the measurements. The analysis shows that the variation in pH of the solution (6.0<pH<9.4) results in considerable changes for τ_{reb} from 0.36 ns (at pH=8.5) up to 0.5 ns (pH=6.0) but effects slightly on the time τ_{esc} (τ_{esc} ~ 0.88 ns).

physics.bio-ph↗