All posts under category "Physics / Physics.bio-Ph"
Based on a multi-agent model, we investigate how target waves emerge from a population dynamics with cyclical interactions among three species. We show that the periodically injecting source in a small central area can generate target waves in a two-dimensional lattice system. By detecting the tempo
We study the interplay between traveling action potentials and spatial inhomogeneities in the FitzHugh-Nagumo model to investigate possible mechanisms for the occurrence of fibrillatory states in the atria of the heart. Different dynamical patterns such as ectopic foci, localized and meandering spir
Since laws of physics exist in nature, their possible relationship to terrestial growth is introduced. By considering the human body as a dynamic system of variable mass (and volume), growing under a gravity field, it is shown how natural laws may influence the vertical growth of humans. This approa
A new type of diode that is made entirely of electrically excitable muscle cells and nonexcitable fibroblast cells is designed, fabricated, and characterized. These two cell types in a rectangular pattern allow the signal initiated on the excitable side to pass to the nonexcitable side, and not in t
Aging is a fundamental aspect of living systems that undergo a progressive deterioration of physiological function with age and an increase of vulnerability to disease and death. Living systems, known as complex systems, require complexity in interactions among molecules, cells, organs, and individu
In many applications expectation values are calculated by partitioning a single experimental time series into an ensemble of data segments of equal length. Such single trajectory ensemble (STE) is a counterpart to a multiple trajectory ensemble (MTE) used whenever independent measurements or realiza
Here is suggested a solution to the accommodation-vergence mismatch problem in 3D stereoscopic displays. It can be achieved by compensating the mismatched focal length with refractive power of adjustable-focus 3D glasses. The compensation would make vergence of human eyes match with position of virt
In the recent paper of Valleriani {it et al} [Phys. Rev. E {bf 83}, 042903 (2011)], a simple model for describing the translation of messenger RNA (mRNA) by ribosomes is presented, and an expression of the translational ratio $r$, defined as the ratio of translation rate $omega_{rm tl}$ of protein f
We revisit the classical problem of nucleated polymerisation and derive a range of exact results describing polymerisation in systems intermediate between the well-known limiting cases of a reaction starting from purely soluble material and for a reaction where no new growth nuclei are formed.
The influence of a single walled carbon nanotube on the structure of a cholesterol cluster (domain) developed over the surface of the endothelial protein 1LQV has been investigated using the classical molecular dynamics (MD) simulation technique. We have observed a substantial impact of carbon nanot
Sequences of events in noise-driven excitable systems with slow variables often show serial correlations among their intervals of events. Here, we employ a master equation for general non-renewal processes to calculate the interval and count statistics of superimposed processes governed by a slow ad
We show that the critical mass M_c=8pi of bacterial populations in two dimensions in the chemotactic problem is the counterpart of the critical temperature T_c=GMm/4k_B of self-gravitating Brownian particles in two-dimensional gravity. We obtain these critical values by using the Virial theorem or b
We investigate in detail the model of a trophic web proposed by Amaral and Meyer [Phys. Rev. Lett. 82, 652 (1999)]. We focused on small-size systems that are relevant for real biological food webs and for which the fluctuations are playing an important role. We show, using Monte Carlo simulations, t
The effects of the finite size of the network on the evolutionary dynamics of a Boolean network are analyzed. In the model considered, Boolean networks evolve via a competition between nodes that punishes those in the majority. It is found that finite size networks evolve in a fundamentally differen
By exerting mechanical force it is possible to unfold/refold RNA molecules one at a time. In a small range of forces, an RNA molecule can hop between the folded and the unfolded state with force-dependent kinetic rates. Here, we introduce a mesoscopic model to analyze the hopping kinetics of RNA hai
To avoid pathological platelet aggregation by von Willebrand factor (VWF), VWF multimers are regulated in size and reactivity for adhesion by ADAMTS13-mediated proteolysis in a shear flow dependent manner. We examined if tensile stress in VWF under shear flow activates the VWF A2 domain for cleavage
The spread of sexually transmitted diseases (e.g. Chlamydia, Syphilis, Gonorrhea, HIV) across populations is a major concern for scientists and health agencies. In this context, both data collection on sexual contact networks and the modeling of disease spreading, are intensively contributing to the
The work presented in this paper essentially focuses at providing a scientific theory to explain the growth of information bearing molecules (size and information contents) without the need of any enzymatic system. It infers the footprints of molecular evolution in the cell interior for a property c
In this note, we address formally the issue of symmetry for probabilities of different dynamical pathways in the forward and reverse directions of a conformational transition. Our discussion is based on a decomposition of equilibrium into opposing steady states, and makes clear the conditions necess
PDZ domains are typical examples of binding motifs mediating the formation of protein-protein assemblies in many different cells. A quantitative characterization of the mechanisms intertwining structure, chemistry and dynamics with the PDZ function represent a challenge in molecular biology. Here we
Experiments in many fields of science and engineering yield data in the form of time series. The Fourier and wavelet transform-based nonparametric methods are used widely to study the spectral characteristics of these time series data. Here, we extend the framework of nonparametric spectral methods
DNA microarrays are devices that are able, in principle, to detect and quantify the presence of specific nucleic acid sequences in complex biological mixtures. The measurement consists in detecting fluorescence signals from several spots on the microarray surface onto which different probe sequences
Plasmodium of emph{Physarum polycephalum} is a single cell visible by unaided eye. On a non-nutrient substrate the plasmodium propagates as a traveling localization, as a compact wave-fragment of protoplasm. The plasmodium-localization travels in its originally predetermined direction for a substant
A mechanism for relationship of solvent viscosity with reaction rate constant at enzyme action is suggested. It is based on fluctuations of electric field in enzyme active site produced by thermally equilibrium rocking (cranckshaft motion) of the rigid plane (in which the dipole moment $approx 3.6 D
Chromatin organization and dynamics is studied in this work at scales ranging from single nucleosome to nucleosomal array by using a unique combination of biochemical assays, single molecule imaging technique and numerical modeling. We demonstrate that a subtle modification in the nucleosome structu
KIF1A kinesins are single-headed motor proteins which move on cylindrical nano-tubes called microtubules (MT). A normal MT consists of 13 protofilaments on which the equispaced motor binding sites form a periodic array. The collective movement of the kinesins on a MT is, therefore, analogous to vehi
The infection pathway of virus in cytoplasm of a living cell is studied from the viewpoint of diffusion theory. The cytoplasm plays a role of a medium for stochastic motion of the virus contained in the endosome as well as the free virus. It is experimentally known that the exponent of anomalous dif
Micro-sized cold atmospheric plasma (uCAP) has been developed to expand the applications of CAP in cancer therapy. In this paper, uCAP devices with different nozzle lengths were applied to investigate effects on both brain (glioblastoma U87) and breast (MDA-MB-231) cancer cells. Various diagnostic t
It has been argued that cellphones are safe because a single microwave photon does not have enough energy to break a chemical bond. We show that cellphone technology operates in the classical wave limit, not the single photon limit. Based on energy densities relative to thermal energy, we estimate t
We investigate the slow time scales that arise from aging of the paths during the process of path aggregation. This is studied using Monte-Carlo simulations of a model aiming to describe the formation of fascicles of axons mediated by contact axon-axon interactions. The growing axons are represented
Experimental variables of optical tweezers instrumentation that affect RNA folding/unfolding kinetics were investigated. A model RNA hairpin, P5ab, was attached to two micron-sized beads through hybrid RNA/DNA handles; one bead was trapped by dual-beam lasers and the other was held by a micropipette
Biodiversity is essential to the viability of ecological systems. Species diversity in ecosystems is promoted by cyclic, non-hierarchical interactions among competing populations. Such non-transitive relations lead to an evolution with central features represented by the `rock-paper-scissors' game,
We present a mathematical analysis of a networks with Integrate-and-Fire neurons and adaptive conductances. Taking into account the realistic fact that the spike time is only known within some textit{finite} precision, we propose a model where spikes are effective at times multiple of a characterist
This report presents the application of polynomial regression for estimating free energy differences using thermodynamic integration. We employ linear regression to construct a polynomial that optimally fits the thermodynamic integration data, and thus reduces the bias and uncertainty of the resulti
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 cycl
We report experimental results on unidirectional traffic-like collective movement of ants on trails. Our work is primarily motivated by fundamental questions on the collective spatio-temporal organization in systems of interacting motile constituents driven far from equilibrium. Making use of the an
The eye lens is the most characteristic example of mammalian tissues exhibiting complex colloidal behaviour. In this paper we briefly describe how dynamics in colloidal suspensions can help addressing selected aspects of lens cataract which is ultimately related to the protein self-assembly under pa
We present a quantitative model for the biological evolution of species body masses within large groups of related species, e.g., terrestrial mammals, in which body mass M evolves according to branching (speciation), multiplicative diffusion, and an extinction probability that increases logarithmica
During fast locomotion - gallop, half bound - of quadruped mammals, the ground contact of the limbs in each pair do not alternate symmetrically. Animals using such asymmetrical gait thus choose whether the left or the right limb will contact the ground first, and this gives rise to limb preference.
Energy transfer (relaxation) phenomena are ubiquitous in nature. At a macroscopic level, the phenomenological theory of heat (Fourier law) successfully describes heat transfer and energy flow. However, its microscopic origin is still under debate. This is because the phenomena can contain many-body,
The Hill coefficient is often used as a direct measure of the cooperativity of binding processes. It is an essential tool for probing properties of reactions in many biochemical systems. Here we analyze existing experimental data and demonstrate that the Hill coefficient characterizing the binding o
Electroencephalogram (EEG) signals are often corrupted with unintended artifacts which need to be removed for extracting meaningful clinical information from them. Typically a priori knowledge of the nature of the artifacts is needed for such purpose. Artifact contamination of EEG is even more promi
We present a simple and emph{non-invasive} experimental procedure to measure the linear viscoelastic properties of cells by passive video particle tracking microrheology. In order to do this, a generalised Langevin equation is adopted to relate the time-dependent thermal fluctuations of a bead, chem
Coherent diffraction imaging (CDI) allows the retrieval of the structure of an isolated object, such as a macromolecule, from its diffraction pattern. CDI requires the fulfilment of two conditions: the imaging radiation must be coherent and the object must be isolated. We discuss that it is possible
We analyze theoretically the problem of cargo transport along microtubules by motors of two species with opposite polarities. We consider two different one-dimensional models previously developed in the literature. On the one hand, a quite widespread model which assumes equal force sharing, here ref
Nuclear pore complexes (NPCs) are very selective filters that monitor the transport between the cytoplasm and the nucleoplasm. Two models have been suggested for the plug of the NPC. They are (i) it is a reversible hydrogel or (ii) it is a polymer brush. We propose a mesoscopic model for the transpo
Blood system functions are very diverse and important for most processes in human organism. One of its primary functions is matter transport among different parts of the organism including tissue supplying with oxygen, carbon dioxide excretion, drug propagation etc. Forecasting of these processes un
We study the passage times of a translocating polymer of length $N$ in three dimensions, while it is pulled through a narrow pore with a constant force $F$ applied to one end of the polymer. At small to moderate forces, satisfying the condition $FN^{nu}/k_BTlesssim1$, where $nuapprox0.588$ is the Fl
Aggregates of twisted protein fibers, such as sickle hemoglobin and actin, are important examples of biopolymers in which elastic interactions play a crucial role in determining the (metastable) bundle radii. Here, we present a corrected version of analysis on the stability of sickle hemoglobin fibe
Synthesis of protein molecules in a cell are carried out by ribosomes. A ribosome can be regarded as a molecular motor which utilizes the input chemical energy to move on a messenger RNA (mRNA) track that also serves as a template for the polymerization of the corresponding protein. The forward move
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