生物物理
Morphogens are secreted signaling molecules that mediate tissue patterning and growth of embryonic tissues. They are secreted in a localized region and spread through the tissue to form a graded concentration profile. We present a…
We propose a general statistical mechanics framework for the collective motion of animals. The framework considers the principle of maximum entropy, the interaction, boundary, and desire effects, as well as the time-delay effect. These…
The theory of chemical kinetics form the basis to describe the dynamics of chemical systems. Owing to physical and thermodynamic constraints, chemical reaction systems possess various structures, which can be utilized to characterize…
The T cell arm of the adaptive immune system provides the host protection against unknown pathogens by discriminating between host and foreign material. This discriminatory capability is achieved by the creation of a repertoire of cells…
Trajectories from a pair of interacting zebrafish are used to test for the existence of anticipatory dynamics in natural systems. Anticipatory dynamics (AD) is unusual in that causal events are not necessarily ordered by their temporal…
ECM components, such as the Perineuronal net (PNN), one of the most prevalent parts surrounding the neuronal cell. PNN is a protective net-like structure regulating neuronal activity such as neurotransmission, charge balance and generates…
The gut microbiota features important genetic diversity, and the specific spatial features of the gut may shape evolution within this environment. We investigate the fixation probability of neutral bacterial mutants within a minimal model…
Kinesin-1 is an ATP-driven, two-headed motor protein that transports intracellular cargoes along microtubule. Based on recent experimental observations, we formulate a mechanochemical model for it, in which forward/backward/futile cycle of…
The process of polarization determines the head and tail of single cells. A mechanism of this kind frequently precedes the subsequent cell locomotion and it determines the direction of motion. The process of polarization has frequently been…
We study a binary mixture of disk-shaped {\it active run and tumble } particles (${ARNPs}$) and passive particles on a two-dimensional substrate. Both types of particles are athermal. The particles interact through the soft repulsive…
Evolution of the amino acid sequences of transthyretin (TTR) can provide additional information about its dynamics that both complements and extends the already extensive static structural data. Protein dynamics is largely driven by…
Avian hair cells depend on electrical resonance for frequency selectivity. The upper bound of the frequency range is limited by the RC time constant of hair cells because the sharpness of tuning requires that the resonance frequency must be…
Experiments by Chretien and co-workers suggest that mitochondria are 10oC hotter than their surroundings. Steady-state theoretical estimates place this difference at a maximum of 10^-5 oC. This million-fold disagreement may be called the…
Ion channels are important proteins for physiological information transfer and functional control. To predict the microscopic origins of their voltage-conductance characteristics, we here applied dissipation-corrected targeted Molecular…
We present the novel approach to mathematical modeling of information processes in biosystems. It explores the mathematical formalism and methodology of quantum theory, especially quantum measurement theory. This approach is known as {\it…
No systematic method exists to derive intra-chromosomal potentials between nucleosomes along a chromosome consistently across a given genome. Such potentials can yield information on nucleosomal ordering, thermal as well as mechanical…
We consider the dynamics of a rigid filament in a motor protein assay under external loading. The motor proteins are modeled as active harmonic linkers with tail ends immobilized on a substrate. Their heads attach to the filament…
An effective implementation of enhanced sampling algorithms for molecular dynamics simulations requires a priori knowledge of the approximate reaction coordinate describing the relevant mechanisms in the system. Here we demonstrate how the…
Spatial organization of chromatin plays a critical role in genome regulation. Various types of affinity mediators and enzymes have been attributed to regulate spatial organization of chromatin from a thermodynamics perspective. However, at…
The dynamics of single red blood cells (RBCs) determine microvascular blood flow by adapting their shape to the flow conditions in the narrow vessels. In this study, we explore the dynamics and shape transitions of RBCs on the cellular…