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arXiv2008

Solution Poisson-Boltzmann equation: Application in the Human Neuron Membrane

With already demonstrated in previous work the equations that describe the space dependence of the electric potential are determined by the solution of the equation of Poisson-Boltzmann. In this work we consider these solutions for the membrane of the human neuron, using a model simplified for this structure considering the distribution of electrolytes in each side of the membrane, as well as the effect of glycocalyx and the lipidic bilayer. It was assumed that on both sides of the membrane the charges are homogeneously distributed and that the potential depends only on coordinate z.

physics.bio-ph↗

arXiv2008

A library-based Monte Carlo technique enables rapid equilibrium sampling of a protein model with atomistic components

There is significant interest in rapid protein simulations because of the time-scale limitations of all-atom methods. Exploiting the low cost and great availability of computer memory, we report a Monte Carlo technique for incorporating fully flexible atomistic protein components (e.g., peptide planes) into protein models without compromising sampling speed or statistical rigor. Building on existing approximate methods (e.g., Rosetta), the technique uses pre-generated statistical libraries of all-atom components which are swapped with the corresponding protein components during a simulation. The simple model we study consists of the three all-atom backbone residues -- Ala, Gly, and Pro -- with structure-based (Go-like) interactions. For the five different proteins considered in this study, LBMC can generate at least 30 statistically independent configurations in about a month of single CPU time. Minimal additional cost is required to add residue-specific interactions.

physics.bio-ph↗

arXiv2009

Dipole emission and coherent transport in random media I

This is the first of a series of papers devoted to develop a microscopical approach to the dipole emission process and its relation to coherent transport in random media. In this Letter, we deduce general expressions for the decay rate of spontaneous emitters and the power emission of induced dipoles embedded in homogenous dielectric media. We derive formulae which apply generically to virtual cavities and, in the continuum approximation, to small real cavities.

physics.optics↗

arXiv2008

Modeling Microscopic Chemical Sensors in Capillaries

Nanotechnology-based microscopic robots could provide accurate in vivo measurement of chemicals in the bloodstream for detailed biological research and as an aid to medical treatment. Quantitative performance estimates of such devices require models of how chemicals in the blood diffuse to the devices. This paper models microscopic robots and red blood cells (erythrocytes) in capillaries using realistic distorted cell shapes. The models evaluate two sensing scenarios: robots moving with the cells past a chemical source on the vessel wall, and robots attached to the wall for longer-term chemical monitoring. Using axial symmetric geometry with realistic flow speeds and diffusion coefficients, we compare detection performance with a simpler model that does not include the cells. The average chemical absorption is quantitatively similar in both models, indicating the simpler model is an adequate design guide to sensor performance in capillaries. However, determining the variation in forces and absorption as cells move requires the full model.

cs.RO↗

arXiv2008

Collective dynamics of water in the living cell and in bulk liquid. New physical models and biological inferences

In the frame of collective dynamics in water, models built on elementary excitations and long-range electromagnetic interactions in the cell and bulk liquid are presented. Making use of the low effective mass of water coherence domains (CDs), we examined the relevance of simple quantum models to cellular characteristics. A hypothesis of CDs Bose-type condensation, and models of CD in spherical wells with impenetrable and semipenetrable walls, and of an isotropic oscillator consisting of two interacting CDs were investigated. Estimated cellular volumes matched to medium-sized bacteria and small prokaryotes, and to some organelles in eukaryotic cells. Also, the cytotoxic effects of heavy water in eukaryotes were explained. In another approach we proposed a plasmon-like model of hydrogen-oxygen ionic plasma in liquid water. In addition to plasmonic oscillations, the model predicted sound-like non-equilibrium elementary excitations that we called densitons (the sound anomaly of water), the vaporization heat and the permittivity dispersion, in agreement to experimental data. The fields generated by ionic plasma oscillations in living cells may support long distance intercellular correlations.

physics.bio-ph↗

arXiv2009

RNA polymerase motor on DNA track: effects of interactions, external force and torque

RNA polymerase (RNAP) is a mobile molecular workshop that polymerizes a RNA molecule by adding monomeric subunits one by one, while moving step by step on the DNA template itself. Here we develop a theoretical model by incorporating the steric interactions of the RNAPs and their mechanochemical cycles which explicitly captures the cyclical shape changes of each motor. Using this model, we explain not only the dependence of the average velocity of a RNAP on the externally applied load force, but also predict a {\it nonmotonic} variation of the average velocity on external torque. We also show the effect of steric interactions of the motors on the total rate of RNA synthesis. In principle, our predictions can be tested by carrying out {\it in-vitro} experiments which we suggest here.

physics.bio-ph↗

arXiv2009

Bidirectional cooperative motion of myosin-II motors on actin tracks with randomly alternating polarities

The cooperative action of many molecular motors is essential for dynamic processes such as cell motility and mitosis. This action can be studied by using motility assays in which the motion of cytoskeletal filaments over a surface coated with motor proteins is tracked. In previous studies of actin-myosin II systems, fast directional motion was observed, reflecting the tendency of myosin II motors to propagate unidirectionally along actin filaments. Here, we present a motility assay with actin bundles consisting of short filamentous segments with randomly alternating polarities. These actin tracks exhibit bidirectional motion with macroscopically large time intervals (of the order of several seconds) between direction reversals. Analysis of this bidirectional motion reveals that the characteristic reversal time, $τ_{rev}$, does not depend on the size of the moving bundle or on the number of motors, $N$. This observation contradicts previous theoretical calculations based on a two-state ratchet model [Badoual et al., Proc. Natl. Acad. Sci. USA, vol. 99, p. 6696 (2002)], predicting an exponential increase of $τ_{rev}$ with $N$. We present a modified version of this model that takes into account the elastic energy due to the stretching of the actin track by the myosin II motors. The new model yields a very good quantitative agreement with the experimental results.

cond-mat.soft↗

arXiv2009

Dynamics of the bacterial flagellar motor with multiple stators - Supporting Information

In this supporting information we briefly describe the torque-speed measurement procedure. We show the hook spring compliance used in the simulations. We analyze the distribution functions of the moving and waiting time intervals. We study the dependence of the torque plateau region on the stator jumping rate and the cutoff angle, and the robustness of the results against different rotor-stator- potential and load-rotor forces.

q-bio.SC↗

arXiv2012

Whilst this Planet Has Gone Cycling On: What Role for Periodic Astronomical Phenomena in Large Scale Patterns in the History of Life?

One of the longstanding debates in the history of paleontology focuses on the issue of whether or not there have been long term cycles (operating over tens of millions of years) in biodiversity and extinction. Here we consider the history of this debate by connecting the skein from Grabau up to 2008. We focus on the evidence for periodicity that has emerged thus far, and conclude that there is indeed some evidence that periodicity may be real, though of course more work is needed. We also comment on possible causal mechanisms, focusing especially on the motion of our solar system in the Galaxy. Moreover, we consider the reasons why some scientists have opposed periodicity over the years. Finally, we consider the significance of this for our understanding of evolution and the history of life.

astro-ph.EP↗

arXiv2009

Absolute free energies estimated by combining pre-calculated molecular fragment libraries

The absolute free energy -- or partition function, equivalently -- of a molecule can be estimated computationally using a suitable reference system. Here, we demonstrate a practical method for staging such calculations by growing a molecule based on a series of fragments. Significant computer time is saved by pre-calculating fragment configurations and interactions for re-use in a variety of molecules. We employ such fragment libraries and interaction tables for amino acids and capping groups to estimate free energies for small peptides. Equilibrium ensembles for the molecules are generated at no additional computational cost, and are used to check our results by comparison to standard dynamics simulation.

physics.bio-ph↗

arXiv2009

Existence of biological uncertainty principle implies that we can never find 'THE' measure for biological complexity

There are innumerable 'biological complexity measure's. While some patterns emerge from these attempts to represent biological complexity, a single measure to encompass the seemingly countless features of biological systems, still eludes the students of Biology. It is the pursuit of this paper to discuss the feasibility of finding one complete and objective measure for biological complexity. A theoretical construct (the 'Thread-Mesh model') is proposed here to describe biological reality. It segments the entire biological space-time in a series of different biological organizations before modeling the property space of each of these organizations with computational and topological constructs. Acknowledging emergence as a key biological property, it has been proved here that the quest for an objective and all-encompassing biological complexity measure would necessarily end up in failure. Since any study of biological complexity is rooted in the knowledge of biological reality, an expression for possible limit of human knowledge about ontological biological reality, in the form of an uncertainty principle, is proposed here. Two theorems are proposed to model the fundamental limitation, owing to observer dependent nature of description of biological reality. They explain the reasons behind failures to construct a single and complete biological complexity measure. This model finds support in various experimental results and therefore provides a reliable and general way to study biological complexity and biological reality.

q-bio.OT↗

arXiv2009

Opening a hydrophobic gate: the nicotinic acetylcholine receptor as an example

To what extent must a hydrophobic gate expand for the channel to count as open? We address this question using the nicotinic acetylcholine receptor (nAChR) as the exemplar. The nAChR is an integral membrane protein which forms a cation selective channel gated by neurotransmitter binding to its extracellular domain. A hydrophobic gating model has been proposed for the nAChR, whereby the pore is incompletely occluded in the closed state channel, with a narrow hydrophobic central gate region which presents an energetic barrier to ion permeation. The nAChR pore is lined by a parallel bundle of five M2 alpha-helices, with the gate formed by three rings of hydrophobic sidechains (9', 13', and 17' of M2). A number of models have been proposed to describe the nature of the conformational change underlying the closed to open transition of the nAChR. These models involve different degrees of M2 helix displacement, rotation, and/or kinking. In this study, we use a simple pore expansion method (previously used to model opening of potassium channels) to generate a series of progressively wider models of the nAChR transmembrane domain. Continuum electrostatics calculations are used to assess the change in the barrier height of the hydrophobic gate as a function of pore expansion. The results suggest that an increase in radius of Delta r ~ 1.5 angstrom is sufficient to functionally open the pore without, for example, a requirement for rotation of the M2 helices. This is evaluated in the context of current mutational and structural data on the nAChR and its homologues.

q-bio.BM↗

arXiv2009

Physical Properties of Biological Membranes

Biological membranes mainly consist of lipids and proteins. While the proteins have many functions as single molecules, the membrane as a whole displays physical properties that cannot be explained on the single molecule level. For example, membranes show melting events, phase behavior, and elasticity. Biomembranes adapt their composition such that the physical properties are maintained when the external conditions change. This gives a role to changes in composition, to temperature and pressure. This article introduces into the physics of membranes as a whole and shows how phenomena as permeability, pulse propagation and the effect of anesthetics arise.

physics.bio-ph↗

arXiv2009

Indisputable facts when implementing spiking neuron networks

In this article, our wish is to demystify some aspects of coding with spike-timing, through a simple review of well-understood technical facts regarding spike coding. The goal is to help better understanding to which extend computing and modelling with spiking neuron networks can be biologically plausible and computationally efficient. We intentionally restrict ourselves to a deterministic dynamics, in this review, and we consider that the dynamics of the network is defined by a non-stochastic mapping. This allows us to stay in a rather simple framework and to propose a review with concrete numerical values, results and formula on (i) general time constraints, (ii) links between continuous signals and spike trains, (iii) spiking networks parameter adjustments. When implementing spiking neuron networks, for computational or biological simulation purposes, it is important to take into account the indisputable facts here reviewed. This precaution could prevent from implementing mechanisms meaningless with regards to obvious time constraints, or from introducing spikes artificially, when continuous calculations would be sufficient and simpler. It is also pointed out that implementing a spiking neuron network is finally a simple task, unless complex neural codes are considered.

q-bio.NC↗

arXiv2009

On-chip manipulation of magnetic nanoparticles through domain walls conduits

The manipulation of geometrically constrained magnetic domain walls (DWs) in nanoscale magnetic strips has attracted much interest recently, with proposals for prospective memory and logic devices. Here we propose to use the high controllability of the motion of geometrically constrained DWs for the manipulation of individual nanoparticles on a chip with an active control of position at the nanometer scale. The proposed method exploits the fact that magnetic nanoparticles in solution can be captured by a DW, whose position can be manipulated with nanometric accuracy in a specifically designed magnetic nanowire structure. We show that the high control over DW nucleation, displacement, and annihilation processes in such structures can be used to capture, transport and release magnetic nanoparticles. As magnetic particles with functionalized surfaces are commonly used as molecule carriers or labels, the accurate control over the handling of the single magnetic nanoparticle is crucial for several applications including single molecule manipulation, separation, cells manipulation and biomagnetic sensing.

physics.bio-ph↗

arXiv2009

Precision and Stability Issues in VBL, the Virtual Biophysics Lab simulation program

The network of biochemical reactions inside living organisms is characterized by an overwhelming complexity which stems from the sheer number of reactions and from the complicated topology of biochemical cycles. However the high speed of computers and the sophisticated computational methods that are available today are powerful tools that allow the numerical exploration of these exceedingly interesting dynamical systems. We are now developing a program, the Virtual Biophysics Lab (VBL), that simulates tumor spheroids, and which includes a reduced - but still quite complex - description of the biochemistry of individual cells, plus many diffusion processes that bring oxygen and nutrients into cells and metabolites into the environment. Each simulation step requires the integration of nonlinear differential equations that describe the individual cell's clockwork and the integration of the diffusion equations. These integrations are carried out under widely different conditions, in a changing environment, and for this reason they need integrators that are both unconditionally stable and that do not display unwanted algorithmic artifacts. These conditions are not always fulfilled in the existing literature, and we feel that a review of the underlying mathematical principles may be important not just for us but for other workers in the field of system biology as well.

physics.bio-ph↗

arXiv2011

A first-passage-time theory for search and capture of chromosomes by microtubules in mitosis

The mitotic spindle is an important intermediate structure in eukaryotic cell division, in which each of a pair of duplicated chromosomes is attached through microtubules to centrosomal bodies located close to the two poles of the dividing cell. Several mechanisms are at work towards the formation of the spindle, one of which is the `capture' of chromosome pairs, held together by kinetochores, by randomly searching microtubules. Although the entire cell cycle can be up to 24 hours long, the mitotic phase typically takes only less than an hour. How does the cell keep the duration of mitosis within this limit? Previous theoretical studies have suggested that the chromosome search and capture is optimized by tuning the microtubule dynamic parameters to minimize the search time. In this paper, we examine this conjecture. We compute the mean search time for a single target by microtubules from a single nucleating site, using a systematic and rigorous theoretical approach, for arbitrary kinetic parameters. The result is extended to multiple targets and nucleating sites by physical arguments. Estimates of mitotic time scales are then obtained for different cells using experimental data. In yeast and mammalian cells, the observed changes in microtubule kinetics between interphase and mitosis are beneficial in reducing the search time. In {\it Xenopus} extracts, by contrast, the opposite effect is observed, in agreement with the current understanding that large cells use additional mechanisms to regulate the duration of the mitotic phase.

q-bio.SC↗

arXiv2010

Single-molecule imaging of protein adsorption mechanisms to surfaces

Protein-surface interactions cause the desirable effect of controlled protein adsorption onto biodevices as well as the undesirable effect of protein fouling. The key to controlling protein-surface adsorptions is to identify and quantify the main adsorption mechanisms: adsorptions that occur (1) while depositing a protein solution onto dry surfaces and (2) after the deposition onto wet surfaces. Bulk measurements cannot reveal the dynamic protein adsorption pathways and thus cannot differentiate between the two adsorption mechanisms. We imaged the interactions of single streptavidin molecules with hydrophobic fused-silica surfaces in real-time. We observed both adsorbed proteins on surfaces and diffusing proteins near surfaces and analyzed their adsorption kinetics. Our analysis shows that the protein solution deposition process is the primary mechanism of streptavidin adsorption onto surfaces at the sub-nanomolar to nanomolar protein concentrations. Furthermore, we found that hydrophilic fused-silica surfaces can prevent the adsorption of streptavidin molecules.

physics.bio-ph↗