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The endoplasmic reticulum (ER), a cellular organelle that forms a cell-spanning network of tubes and sheets, is an important location of protein synthesis and folding. When the ER experiences sustained unfolded protein stress, IRE1 proteins embedded in the ER membrane activate and assemble into clusters as part of the...
We compute absolute binding affinities for two ligands bound to the FKBP protein using non-equilibrium unbinding simulations. The methodology is straight-forward, requiring little or no modification to many modern molecular simulation packages.
A structural understanding of whole cells in three dimensions at high spatial resolution remains a significant challenge and, in the case of X-rays, has been limited by radiation damage. By alleviating this limitation, cryogenic coherent diffraction imaging (cryo-CDI) could bridge the important resolution gap between ...
We propose that protein loops can be interpreted as topological domain-wall solitons. They interpolate between ground states that are the secondary structures like alpha-helices and beta-strands.
The time for a DNA sequence to find its homologous depends on a long random search process inside the cell nucleus. Using polymer models, we model and compute here the mean first encounter time (MFET) between two sites located on two different polymer chains and confined by potential wells.
Biological cells in living tissues form dynamic patterns with local orientational order and topological defects. Here we demonstrate an approach to produce cell monolayer with the predesigned orientational patterns using human dermal fibroblast cells (HDF) placed onto a photoaligned liquid crystal elastomer (LCE).
We unzip DNA molecules using optical tweezers and determine the sizes of the cooperatively unzipping and zipping regions separating consecutive metastable intermediates along the unzipping pathway. Sizes are found to be distributed following a power law, ranging from one base pair up to more than a hundred base pairs....
Feedback in sensory biochemical networks can give rise to bifurcations in cells' behavioral response. These bifurcations share many properties with thermodynamic critical points.
The Geant4-DNA project proposes to develop an open-source simulation software based and fully included in the general-purpose Geant4 Monte Carlo simulation toolkit. The main objective of this software is to simulate biological damages induced by ionising radiation at the cellular and sub-cellular scale.
While the dynamics of a fully flexible polymer ejecting a capsid through a nanopore has been extensively studied, the ejection dynamics of semiflexible polymers has not been properly characterized. Here we report results from simulations of ejection dynamics of semiflexible polymers ejecting from spherical capsids.
We propose a PDE-constrained shape registration algorithm that captures the deformation and growth of biological tissue from imaging data. Shape registration is the process of evaluating optimum alignment between pairs of geometries through a spatial transformation function.
Chemically or optically powered active matter plays an increasingly important role in materials design but its computational potential has yet to be explored systematically. The competition between energy consumption and dissipation imposes stringent physical constraints on the information transport in active flow net...
We present a model of the infection of Hantavirus in deer mouse, Peromyscus maniculatus, based on biological observations of the system in the North American Southwest. The results of the analysis shed light on relevant observations of the biological system, such as the sporadical disappearance of the infection, and t...
In an adiabatically shielded system the total enthalpy is conserved. Enthalpy fluctuations of an arbitrarily chosen subsystem must be buffered by the remainder of the total system which serves as a heat reservoir.
Based on the understanding that chemical bonds can act as tunnel junctions in the Coulomb blockade regime, and on the technical ability to coat a DNA strand with metal, we suggest that DNA can be used to built logical devices. We discuss two explicit examples: a Single Electron Tunneling Transistor (SET) and a Quantum...
The origin and shape of metabolic scaling has been controversial since Kleiber found that basal metabolic rate of animals seemed to vary as a power law of their body mass with exponent 3/4, instead of 2/3, as a surface-to-volume argument predicts. The universality of exponent 3/4 -claimed in terms of the fractal prope...
Background. In a number of recent experiments with food-and-mouth disease virus, a deleterious mutant, was found to avoid extinction and remain in the population for long periods of time.
In this manuscript we present an in vitro model based on agarose gel that can be used to simulate a dirty, oily, bloody, and morphologically complex surface of, for example, an open wound. We show this models effectiveness in simulating depth of penetration of reactive species generated in plasma deep into tissue of a...
Thermal light sources can produce photons with strong spatial correlations. We study the role that these correlations might potentially play in bacterial photosynthesis.
Microbial colonies are experimental model systems for studying the colonization of new territory by biological species through range expansion. We study a generalization of the two-species Eden model, which incorporates local frequency-dependent selection, in order to analyze how social interactions between two specie...
Blood leukocytes can exhibit extensive morphological changes during their passage through small capillary vessels. The human monocytic THP-1 cell line was used to explore the metabolic dependence of these shape changes.
In the current study, we demonstrated that allostery transpires by entropy transfers across time-spatial scales that actualize the conception of a molecular trap that supervises ligand interaction, selection, and migration into the amphipathic groove of the 14-3-3 {\zeta} docking protein. Ligand binding transpires by ...
When particles move at a constant speed and have the tendency to align their directions of motion, ordered large scale movement can emerge despite significant levels of noise. Many variants of this model of self-propelled particles have been studied to explain the coherent motion of groups of birds, fish or microbes.
Through modelling and simulations we show that material instabilities play a dominant role in the mechanical behavior of the fibrous collagen Extracellular Matrix (ECM), as observed when the ECM is deformed by contractile biological cells. We compare two families of fiber network models, Family 1 with stable and Famil...
We introduce and analyze a model for osmotically spreading biofilm colonies at solid-air interfaces that includes wetting phenomena, i.e. surface forces. The model combines a hydrodynamic description for biologically passive liquid suspensions with bioactive processes.
Microtubules are a major component of the cytoskeleton distinguished by highly dynamic behavior both in vitro and in vivo. We propose a general mathematical model that accounts for the growth, catastrophe, rescue and nucleation processes in the polymerization of microtubules from tubulin dimers.
We introduce the concept of self-tuned criticality as a general mechanism for signal detection in sensory systems. In the case of hearing, we argue that active amplification of faint sounds is provided by a dynamical system which is maintained at the threshold of an oscillatory instability.
Fast, volumetric imaging over large scales has been a long-standing goal in biological microscopy. Scanning techniques such as fluorescence confocal microscopy can acquire 2D images at high resolution and high speed, but extending the acquisition to multiple planes at different depths requires an axial scanning mechan...
Many human diseases are associated with protein aggregation and fibrillation. We present experiments on in vitro glucagon fibrillation using total internal reflection fluorescence microscopy, providing real-time measurements of single-fibril growth.
Eukaryotic cells adhere to extracellular matrix during the normal development of the organism, forming static adhesion as well as during cell motility. We study this process by considering a simplified coarse-grained model of a vesicle that has uniform adhesion energy with a flat substrate, mobile curved membrane prot...
Motivated by recent experiments, we develop a model for DNA toroids under external tension. We find that tori are the equilibrium states for our model up to a critical tension, above which they become only metstable.
We have used kinetic Monte Carlo simulations to study the kinetics of unfolding of cross-linked polymer chains under mechanical loading. As the ends of a chain are pulled apart, the force transmitted by each crosslink increases until it ruptures.
Microswimmers are exposed in nature to crowded environments and their transport properties depend in a subtle way on the interaction with obstacles. Here, we investigate a model for a single ideal circle swimmer exploring a two-dimensional disordered array of impenetrable obstacles.
We have managed to correlate the stability constants of complex formation, which can be registered in equilibrium state, to the dynamic characteristic of the complex lifetime. Thus, the principal concept of molecular biophysics regarding biomolecule, structure-dynamics-function can be reformatted as structure-stabilit...
Collections of cells exhibit coherent migration during morphogenesis, cancer metastasis, and wound healing. In many cases, bigger clusters split, smaller sub-clusters collide and reassemble, and gaps continually emerge.
Short single-walled carbon nanotubes (SWNTs) functionalized by PEGylated phospholipids are biologically non-toxic and long-circulating nanomaterials with intrinsic near infrared photoluminescence (NIR PL), characteristic Raman spectra, and strong optical absorbance in the near infrared (NIR). This work demonstrates th...
A mechanism for creating an enantioenrichment in the amino acids, the building blocks of the proteins, that involves global selection of one handedness by interactions between the amino acids and neutrinos from core-collapse supernovae is described. The chiral selection involves the dependence of the interaction cross...
Neurons transmit active potentials through axons, which are essential for the brain to function. In this study, the axonal networks of the murine brain were visualized with X-ray tomographic microscopy, also known as X-ray microtomography or micro-CT.
The field of biomedical imaging has undergone a rapid growth in recent years, mostly due to the implementation of ad-hoc designed experimental setups, theoretical support methods and numerical reconstructions. Especially for biological samples, the high number of scattering events occurring during the photon propagati...
The biomechanical properties of blood clots, which are dictated by their compositions and micro-structures, play a critical role in determining their fates, occlusion, persistency, or embolization in the human circulatory system. While numerous constitutive models have emerged to describe the biomechanics of blood clo...
Motivated by DNA electrophoresis near a nanopore, we consider the flow field around an "elongated jet", a long thin source which injects momentum into a liquid. This solution qualitatively describes the electro-osmotic flow around a long rigid polymer, where due to electrohydrodynamic coupling, the solvent rec...
Learning from experience is a key feature of decision-making in cognitively complex organisms. Strategic interactions involving Bayesian inferential strategies can enable us to better understand how evolving individual choices to be altruistic or selfish can affect collective outcomes in social dilemmas.
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 adaptation variable.
We develop a field theory-inspired stochastic model for description of tumour growth based on an analogy with an SI epidemic model, where the susceptible individuals (S) would represent the healthy cells and the infected ones (I), the cancer cells. From this model, we obtain a curve describing the tumour volume as a f...
In this report, we present an unsupervised machine learning method for determining groups of molecular systems according to similarity in their dynamics or structures using Ward's minimum variance objective function. We first apply the minimum variance clustering to a set of simulated tripeptides using the informa...
For many membrane proteins the determination of their topology remains a challenge for methods like X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy. Electron paramagnetic resonance (EPR) spectroscopy has evolved as an alternative technique to study structure and dynamics of membrane proteins.
Many spherical viruses encapsulate their genome in protein shells with icosahedral symmetry. This process is spontaneous and driven by electrostatic interactions between positive domains on the virus coat proteins and the negative genome.
We present a general dynamical theory of a membrane coupled to an actin cortex containing polymerizing filaments with active stresses and currents, and demonstrate that active membrane dynamics [Phys. Rev. Lett \textbf{84}, 3494 (2000)] and spontaneous shape oscillations emerge from this description.
Structure fluctuations and conformational changes accompany all biological processes involving macromolecules. The paper presents a classification of protein residues based on the normalized equilibrium fluctuations of the residue centers of mass in proteins and a statistical analysis of conformation changes in the si...
The transfer of electrons and holes along DNA dimers, trimers and polymers is described at the base-pair level, using the relevant on-site energies of the base-pairs and the hopping parameters between successive base-pairs. The temporal and spatial evolution of carriers along a $N$ base-pair DNA segment is determined,...
Recent in vitro experiments have shown that DNA ejection from bacteriophage can be partially stopped by surrounding osmotic pressure when ejected DNA is digested by DNase I on the course of ejection. We argue in this work by combination of experimental techniques (osmotic suppression without DNaseI monitored by UV abs...
The influence of the intramolecular anharmonicity and the strong vibron-phonon coupling on the two-vibron dynamics in an $\alpha$-helix protein is studied within a modified Davydov model. The intramolecular anharmonicity of each amide-I vibration is considered and the vibron dynamics is described according to the smal...
Microorganismal motility is often characterised by complex responses to environmental physico-chemical stimuli. Although the biological basis of these responses is often not well understood, their exploitation already promises novel avenues to directly control the motion of living active matter at both the individual ...
Iron (Fe) reduction is one of Earth's most ancient microbial metabolisms, but after atmosphere-ocean oxygenation, this anaerobic process was relegated to niche anoxic environments below the water and soil surface. However, new technologies to monitor redox processes at the microscale relevant to microbial cells ha...
DNA detection is of great significance in the point-of-care diagnostics. The stiffness of DNA, varying with its sequence and mechanochemical environment, could be a potential marker for DNA identification.
The migratory dynamics of cells in physiological processes, ranging from wound healing to cancer metastasis, rely on contact-mediated cell-cell interactions. These interactions play a key role in shaping the stochastic trajectories of migrating cells.
A simple model of a circularly closed dsDNA in a poor solvent is considered as an example of a semi-flexible polymer with self-attraction. To find the ground states, the conformational energy is computed as a sum of the bending and torsional elastic components and the effective self-attraction energy.
The regulation of cellular function is often controlled at the level of gene transcription. Such genetic regulation usually consists of interacting networks, whereby gene products from a single network can act to control their own expression or the production of protein in another network.
In computational neuroscience, it is common to use the simplifying assumption that diffusive currents are negligible compared to Ohmic currents. However, endured periods of intense neural signaling may cause local ion concentration changes in the millimolar range.
Pennes' differential equation for bioheat transfer and the heat transfer equation are solved for the temperature distribution in a living tissue with spherical inclusions, irradiated by microwave power. It is shown that relative temperature excess in a small inclusion in the tissue in some cases is inversely propo...
We investigate diffusive search on planar networks, motivated by tubular organelle networks in cell biology that contain molecules searching for reaction partners and binding sites. Exact calculation of the diffusive mean first-passage time on a spatial network is used to characterize the typical search time as a func...
We have developed a novel scanning probe-based methodology to study cell biomechanics. The time dependence of the force exerted by the cell surface on a scanning probe at constant local deformation has been used to extract local relaxational responses.
The detection of biomolecules at the single molecular level have important applications in the fields of biosensing and biomedical diagnosis. Solid state nanopore (SS-nanopore) is an effective tool to perform the single molecular detection, due to its unique properties of label-free and less sample consumption.
In the present letter we suggest a new theoretical model for a quantitative description of the magnetoreception mechanism in birds. The considered mechanism involves two types of iron minerals (magnetite and maghemite) which were found in subcellular compartments within sensory dendrites of the upper beak of several b...
We study translocation dynamics of a driven compressible semi-flexible chain consisting of alternate blocks of stiff ($S$) and flexible ($F$) segments of size $m$ and $n$ respectively for different chain length $N$ in two dimension (2D). The free parameters in the model are the bending rigidity $\kappa_b$ which contro...
We consider the influence of a terahertz field on the breathing dynamics of double-stranded DNA. We model the spontaneous formation of spatially localized openings of a damped and driven DNA chain, and find that linear instabilities lead to dynamic dimerization, while true local strand separations require a threshold ...
Recent developments in stimulated emission depletion (STED) microscopy achieved nanometer scale resolution and showed great potential in live cell imaging. Yet, STED nanoscopy techniques are based on single point-scanning.
The nematode Caenorhabditis elegans, with information on neural connectivity, three-dimensional position and cell linage provides a unique system for understanding the development of neural networks. Although C. elegans has been widely studied in the past, we present the first statistical study from a developmental pe...
Enzyme-substrate kinetics form the basis of many biomolecular processes. The interplay between substrate binding and substrate geometry can give rise to long-range interactions between enzyme binding events.
Topological properties of native folds are obtained from statistical analysis of 160 low homology proteins covering the four structural classes. This is done analysing one, two and three-vertex joint distribution of quantities related to the corresponding network of amino acid residues.
Sterols have been ascribed a major role in the organization of biological membranes, in particular for the formation of liquid ordered domains in complex lipid mixtures. Here, we employed molecular dynamics simulations to compare the effects of cholesterol and ergosterol as the major sterol of mammalian and fungal cel...
We develop a general analytical and numerical framework for estimating intra- and extra-neurite water fractions and diffusion coefficients, as well as neurite orientational dispersion, in each imaging voxel. By employing a set of rotational invariants and their expansion in the powers of diffusion weighting, we analyt...
Due to its polyionic character the DNA double helix is stable and biologically active only in salty aqueous media where its charge is compensated by solvent counterions. Monovalent metal ions are ubiquitous in DNA environment and they are usually considered as the possible driving force of sequence-dependent modulatio...
The rapid and global spread of coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), underscored the urgent need for fast, reliable, and adaptable diagnostic tools capable of responding to current and future viral threats. Early diagnosis is key to limiting tr...
Icosahedral virus capsids are composed of symmetrons, organized arrangements of capsomers. There are three types of symmetrons: disymmetrons, trisymmetrons, and pentasymmetrons, which have different shapes and are centered on the icosahedral 2-fold, 3-fold and 5-fold axes of symmetry, respectively.
We study theoretically in the present work the self-assembly of molecules in an open system, which is fed by monomers and depleted in partial or complete clusters. Such a scenario is likely to occur for example in the context of viral self-assembly.
A representation of frequency of strings of length K in complete genomes of many organisms in a square has led to seemingly self-similar patterns when K increases. These patterns are caused by under-represented strings with a certain "tag"-string and they define some fractals when K tends to infinite.
Immune cells learn about their antigenic targets using tactile sense: during recognition, a highly organized yet dynamic motif, named immunological synapse, forms between immune cells and antigen-presenting cells (APCs). Via synapses, immune cells selectively extract recognized antigen from APCs by applying mechanical...
Chirality is considered by many scientists to be mainly a geometric concept. There exists also a physical aspect of chirality which is largely being overlooked at.
Spiral waves are spatial-temporal patterns that can emerge in different systems as heart tissues, chemical oscillators, ecological networks and the brain. These waves have been identified in the neocortex of turtles, rats, and humans, particularly during sleep-like states.
We present a non-invasive, label-free method of imaging blood cells flowing through human capillaries in vivo using oblique back-illumination capillaroscopy (OBC). Green light illumination allows simultaneous phase and absorption contrast, enhancing the ability to distinguish red and white blood cells.
We study the interaction of berberine and sanguinarine (plant alkaloids) with DNA in aqueous solutions, by using optical spectroscopy methods (absorption and fluorescence). The dependencies of alkaloid spectral characteristics on the concentration ratio N/c between the DNA base pairs and alkaloid molecules in the solu...
Many species of millimetric fungus-harvesting termites collectively build uninhabited, massive mound structures enclosing a network of broad tunnels which protrude from the ground meters above their subterranean nests. It is widely accepted that the purpose of these mounds is to give the colony a controlled micro-clim...
To fulfill their killing functions, cytotoxic T lymphocytes (CTLs) need to migrate to search for their target cells in complex biological microenvironments, a key component of which is extracellular matrix (ECM). The mechanisms underlying CTL's navigation are not well understood so far.
Configurational entropy is an important factor in the free energy change of many macromolecular recognition and binding processes, and has been intensively studied. Despite great progresses that have been made, the global sampling remains to be a grand challenge in computational analysis of relevant processes.
In this paper, blood and tissues samples from one normal and one thalassaemic lab-mice were studied using 57Fe Mossbauer spectroscopy at 78K for the first time. In contrast to human patients, these laboratory mice did not receive any medical treatment, thus the iron components present in the samples are not altered.
A discrete rate theory for general multi-ion channels is presented, in which the continuous dynamics of ion diffusion is reduced to transitions between Markovian discrete states. In an open channel, the ion permeation process involves three types of events: an ion entering the channel, an ion escaping from the channel...
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 characteristic time scale $\de...
Protein motions occur on multiple time and distance scales. Large-scale motions of protein tertiary-structure elements, i.e. domains, are particularly intriguing as they are essential for the catalytic activity of many enzymes and for the functional cycles of protein machines and motors.
We present a novel buckling instability relevant to membrane budding in eukaryotic cells. In this mechanism, curved filaments bind to a lipid bilayer without changing its intrinsic curvature.
We present an analysis of six deterministic models for epidemic spreading. The evolution of the number of individuals of each class is given by ordinary differential equations of the first order in time, which are set up by using the laws of mass action providing the rates of the several processes that define each mod...
In this paper, system identification approach has been adopted to develop a novel dynamical model for describing the relationship between light as an environmental stimulus and the electrical response as the measured output for a bay leaf (Laurus nobilis) plant. More specifically, the target is to predict the characte...
We have earlier reported the iMOLSDOCK technique to perform induced-fit peptide-protein docking. iMOLSDOCK uses the mutually orthogonal Latin squares (MOLS) technique to sample the conformation and the docking pose of the small molecule ligand and also the flexible residues of the receptor protein, and arrive at the o...
We have made a preliminary analysis of the results about the eVects on tumoral cell line (lymphoid T cell line Jurkat) induced by UVB radiation (dose of 310 mJ/cm^2) with and without a vegetable mixture. In the present study, we have used two techniques: Fourier transform infrared spectroscopy (FTIR) and flow cytometr...
Drosophila melanogaster hemocytes are highly motile cells that are crucial for successful embryogenesis and have important roles in the organism's immunological response. Hemocyte motion was measured using selective plane illumination microscopy.
Lipid monolayers have been shown to represent a powerful tool in studying mechanical and thermodynamic properties of lipid membranes as well as their interaction with proteins. Using Einstein's theory of fluctuations we here demonstrate, that an experimentally derived linear relationship both between transition en...
We present a weakly coupled map lattice model for patterning that explores the effects exerted by weakening the local dynamic rules on model biological and artificial networks composed of two-state building blocks (cells). To this end, we use two cellular automata models based on:
The dynamic behavior of bundles of actin filaments growing against a loaded obstacle is investigated through a generalized version of the standard multi filaments Brownian Ratchet model in which the (de)polymerizing filaments are treated not as rigid rods but as semi-flexible discrete wormlike chains with a realistic v...
The adoption of digital twins (DTs) in precision medicine is increasingly viable, propelled by extensive data collection and advancements in artificial intelligence (AI), alongside traditional biomedical methodologies. However, the reliance on black-box predictive models, which utilize large datasets, presents limitat...
Tensegrity structures are special architectures made by floating compressed struts kept together by a continuous system of tensed cables. The multiplicity of shapes that tensegrity structures can assume and their intrinsic capability to be deployable and assembled, so storing (and releasing) elastic energy, have motiv...

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