Split (1)

train · 127k rows

text large_stringlengths 7 3.02k
Load-bearing tissues are typically fortified by networks of protein fibers, often with preferential orientations. This fiber structure imparts the tissues with direction-dependent mechanical properties optimized to support specific external loads.
Protein compartmentalization in the frame of a liquid-liquid phase separation is a key mechanism to optimize spatiotemporal control of biological systems. Such a compartmentalization process reduces the intrinsic noise in protein concentration due to stochasticity in gene expression.
In 2005, we proposed that the nerve pulse is an electromechanical soliton. This concept represents a challenge to the well-known Hodgkin-Huxley model which is of a purely electrical nature.
We demonstrate that powder diffraction data can be collected from sub-micron crystals of a mbrane protein with nearly two orders of magnitude more atoms than the molecules commonly used for powder diffraction. The crystals of photosystem-1 protein were size-selected using a 500 nm pore- size filter and delivered to a ...
Main aim of this topical issue is to report recent advances in noisy nonequilibrium processes useful to describe the dynamics of ecological systems and to address the mechanisms of spatio-temporal pattern formation in ecology both from the experimental and theoretical points of view. This is in order to understand the...
Biological molecular machines are enzymes that simultaneously catalyze two processes, one donating free energy and second accepting it. Recent studies show that most native protein enzymes have a rich stochastic dynamics that often manifests in fluctuating rates of the catalyzed processes and the presence of short-ter...
Computer modeling of multicellular systems has been a valuable tool for interpreting and guiding in vitro experiments relevant to embryonic morphogenesis, tumor growth, angiogenesis and, lately, structure formation following the printing of cell aggregates as bioink particles. Computer simulations based on Metropolis ...
We have developed a novel in vitro instrument that can deliver intermediate frequency (100 - 400 kHz), moderate intensity (up to and exceeding 6.5 V/cm pk-pk) electric fields (EFs) to cell and tissue cultures generated using induced electromagnetic fields (EMFs) in a solenoid coil. A major application of these EFs is ...
The melting curves of short heterogeneous DNA chains in solution are calculated on the basis of statistical thermodynamics and compared to experiments. The computation of the partition function is based on the Peyrard-Bishop hamiltonian, which has already been adopted in the theoretical description of the melting of l...
Understanding a neural code requires knowledge both of the elementary symbols that transmit information and of the algorithm for translating these symbols into sensory signals or motor actions. We show that these questions can be separated: the information carried by any candidate symbol in the code--- a pattern of sp...
Because of growing interest in temperature-based sampling methods like replica exchange, this note aims to make some observations and raise some potentially important questions which we have not seen addressed sufficiently in the literature. Mainly, we wish to call attention to limits on the maximum speed-up to be exp...
We present a two-species population model in a well-mixed environment where the dynamics involves, in addition to birth and death, changes due to environmental factors and inter-species interactions. The novel dynamical components are motivated by two common mechanisms for developing antibiotic resistance in bacteria:...
Living organisms have to adjust to their surrounding in order to survive in stressful conditions. We study this mechanism in one of most primitive creatures - photosynthetic green sulfur bacteria.
Cell mechanical functions like locomotion, contraction and division are controlled by the cytoskeleton, a dynamic biopolymer network whose mechanical properties remain poorly understood. We perform single-cell uniaxial stretching experiments on 3T3 fibroblasts.
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 consideri...
We introduce a formulation for normal mode analyses of globular proteins that significantly improves on an earlier, 1-parameter formulation (M. Tirion, PRL 77, 1905 (1996)) that characterized the slow modes associated with protein data bank structures.
We suggest to discriminate single DNA bases via transverse ionic transport, namely by detecting the ionic current that flows in a channel while a single-stranded DNA is driven through an intersecting nanochannel. Our all-atom molecular dynamics simulations indeed show that the ionic currents of the four bases are stat...
The Lévy walk is a non-Brownian random walk model that has been found to describe anomalous dynamic phenomena in diverse fields ranging from biology over quantum physics to ecology. Recurrently occurring problems are to examine whether observed data are successfully quantified by a model classified as Lévy walks or no...
For group-living animals, reaching consensus to stay cohesive is crucial for their fitness, particularly when collective motion starts and stops. Understanding the decision-making at individual and collective levels upon sudden disturbances is central in the study of collective animal behavior, and concerns the broade...
We propose a model for demixing of two species by assuming a density-dependent effective diffusion coefficient of the particles. Both sorts of microswimmers diffuse as active overdamped Brownian particles with a noise intensity that is determined by the surrounding density of the respective other species within a sens...
In the past two decades, under the conditions that both the osmotic pressure $\Delta p$ and tensile stress $\lambda$ equal zero, a rigorous solution (RS) of human red blood cell (RBC) with a minus spontaneous curvature $c_{0}$ has been derived with Helfrich model. And, by fitting with observed shapes of RBC, $c_{0}R_{...
Swimming micro-organisms such as bacteria or spermatozoa are typically found in dense suspensions, and exhibit collective modes of locomotion qualitatively different from that displayed by isolated cells. In the dilute limit where fluid-mediated interactions can be treated rigorously, the long-time hydrodynamics of a ...
The cochlea or inner ear has a remarkable ability to amplify sound signals. This is understood to derive at least in part from some active process that magnifies vibrations of the basilar membrane (BM) and the cochlear partition in which it is embedded, to the extent that it overcomes the effect of viscous damping fro...
Cells moving on a two dimensional substrate generate motion by polymerizing actin filament networks inside a flat membrane protrusion. New filaments are generated by branching off existing ones, giving rise to branched network structures.
We investigate mechanisms which could generate transient monopole signals in measuring current source density (CSD), as it had been indicated to occur in recent small volume experiments. A simple model is defined for this purpose.
Both the translational diffusion coefficient $D$ and the electrophoretic mobility $\mu$ of a short rod-like molecule (such as dsDNA) that is being pulled towards a nanopore by an electric field should depend on its orientation. Since a charged rod-like molecule tends to orient in the presence of an inhomogeneous elect...
Micro-domains of modified surface potential (SP) were created on hydroxyapatite (HAp) films by direct patterning by midenergy focused electron beam, typically available as a microprobe of Scanning Electron Microscopes. The SP distribution of these patterns has been studied on sub-micrometer scale by the Kelvin Probe F...
Most proteins must remain soluble in the cytosol in order to perform their biological functions. To protect against undesired protein aggregation, living cells maintain a population of molecular chaperones that ensure the solubility of the proteome.
Label-free biosensors, including conventional quartz-crystal-microbalance (QCM) biosensor, are seriously affected by nonspecific adsorption of contaminants involved in analyte solution, and it is exceptionally difficult to extract the sensor responses caused only by the targets. In this study, we reveal that this diff...
The fluid shear stress is an important regulator of the cardiovascular system via the endothelium-derived relaxing factor (EDRF) that is Nitric Oxide. This mechanism involves biochemical reactions in an arterial wall.
Spatial information from cell-surface receptors is crucial for processes that require signal processing and sensing of the environment. Here, we investigate the optimal placement of such receptors through a theoretical model that minimizes uncertainty in gradient estimation.
We have studied a spatially extended snowdrift game, in which the players are located on the sites of two-dimensional square lattices and repeatedly have to choose one of the two strategies, either cooperation (C) or defection (D). A player interacts with its nearest neighbors only, and aims at playing a strategy whic...
The folding characteristics of sequences reduced with a possibly simplified representation of five types of residues are shown to be similar to their original ones with the natural set of residues (20 types or 20 letters). The reduced sequences have a good foldability and fold to the same native structure of their opt...
Proteinaceous aggregation occurs through self-assembly-- a process not entirely understood. In a recent article [1], an analytical theory for amyloid fibril growth via secondary rather than primary nucleation was presented.
A detailed stochastic model of single-gene auto-regulation is established and its solutions are explored when mRNA dynamics is fast compared with protein dynamics and in the opposite regime. The model includes all the sources of randomness that are intrinsic to the auto-regulation process and it considers both transcr...
N2 association to the FeMo-cofactor of nitrogenase, including the recently identified central N ligand, has been investigated using first-principles electronic structure calculations. The oxidation state of the resting state of the cofactor and its electronic structure has been identified.
A wide spectrum of Peritrichous bacteria undergo considerable physiological changes when they are inoculated onto nutrition-rich surfaces and exhibit a rapid and collective migration denoted as swarming. Thereby, the length of such swarmer cells and their number of flagella increases substantially.
We discuss the problem of observation of natural similarity in skeletal evolution of terrestrial mammals. Analysis is given by means of testing of the power scaling laws established in long bone allometry, which describe development of bones (of length $L$ and diameter $D$) with body mass in terms of the growth expone...
Recent work has highlighted roles for thermodynamic phase behavior in diverse cellular processes. Proteins and nucleic acids can phase separate into three-dimensional liquid droplets in the cytoplasm and nucleus and the plasma membrane of animal cells appears tuned close to a two-dimensional liquid-liquid critical poi...
Motivated by the observation of non-exponential run-time distributions of bacterial swimmers, we propose a minimal phenomenological model for taxis of active particles whose motion is controlled by an internal clock. The ticking of the clock depends on an external concentration field, e.g. a chemical substance.
This work discusses results of experimental investigations of the specific heat, $C$, of apple in a wide interval of moisture contents ($W=0-0.9$) and temperatures ($T = 283-363$ K). The obtained data reveal the important role of the bound water in determination of $C(W,T)$ behaviour.
Several works reported increased differentiation of neuronal cells grown on graphene; however, the molecular mechanism driving axon elongation on this material has remained elusive. Here, we study the axonal transport of nerve growth factor (NGF), the neurotrophin supporting development of peripheral neurons, as a key...
Microfluidic biosensors have been utilized for sensing a wide range of antigens using numerous configurations. Bead based microfluidic sensors have been a popular modality due to the plug and play nature of analyte choice and the favorable geometry of spherical sensor scaffolds.
We present a graphene/Cu nanoparticle hybrids (G/CuNPs) system as a surface-enhanced Raman scattering (SERS) substrate for adenosine detection. The Cu nanoparticles wrapped around a monolayer graphene shell were directly synthesized on flat quartz by chemical vapor deposition in a mixture of methane and hydrogen.
Recent single-molecule force measurements on single-domain proteins have highlighted a three-state folding mechanism where a stabilized intermediate state (I) is observed on the folding trajectory between the stretched state and the native state. Here we investigate on-lattice protein-like heteropolymer models that le...
During cell division, sister chromatids are segregated by the mitotic spindle, a bipolar assembly of interdigitating antiparallel polar filaments called microtubules. Establishing a stable overlap region is essential for maintenance of bipolarity, but the underlying mechanisms are poorly understood.
As experiments continue to increase in size and scope, a fundamental challenge of subsequent analyses is to recast the wealth of information into an intuitive and readily-interpretable form. Often, each measurement only conveys the relationship between a pair of entries, and it is difficult to integrate these local in...
Whistled speech is a little studied local use of language shaped by several cultures of the world either for distant dialogues or for rendering traditional songs. This practice consists of an emulation of the voice thanks to a simple modulated pitch.
The Turing instability paradigm is revisited in the context of a multispecies diffusion scheme derived from a self-consistent microscopic formulation. The analysis is developed with reference to the case of two species.
We discuss the Surface-Plasmon-Resonance (SPR) technique based on Fourier -Transform - InfraRed (FTIR) spectrometry. We explore the potential of the infrared surface plasmon resonance technique for biological studies in aqueous solutions and compare it to the conventional surface plasmon technique operating in the vis...
We study a theoretical model for the toxin-antitoxin (hok/sok) mechanism for plasmid maintenance in bacteria. Toxin-antitoxin systems enforce the maintenance of a plasmid through post-segregational killing of cells that have lost the plasmid.
We investigate a multi-locus evolutionary model which is based on the DNA shuffling protocol widely applied in \textit{in vitro} directed evolution. This model incorporates selection, recombination and point mutations.
The mechanisms associated with an owls ability to fly silently have been the subject of scientific interest for many decades and a source of inspiration in the context of reducing noise in both flapping and non-flapping flight. Here, we characterize the near wake dynamics and associated flow structures that are produc...
We show that the effect of stress on the reproductive fitness of noisy cell populations can be modelled as first-passage time problem, and demonstrate that even relatively short-lived fluctuations in gene expression can ensure long-term survival of a drug-resistant population. We examine how this effect contributes to...
The probability that an advantageous mutant rises to fixation in a viral quasispecies is investigated in the framework of multi-type branching processes. Whether fixation is possible depends on the overall growth rate of the quasispecies that will form if invasion is successful, rather than on the individual fitness o...
Peritrichous bacteria synchronize and bundle their flagella to actively swim while disruption of the bundle leads to tumbling. It is still not known whether the number of flagella represents an evolutionary adaptation towards optimizing bacterial navigation.
Congestion limits the efficiency of transport networks ranging from highways to the internet. Fungal hyphal networks are studied as an examples of optimal biological transport networks, but the scheduling and direction of traffic to avoid congestion has not been examined.
In this work, we show that by varying the experimental conditions, the driving amplitude, a dynamic force microscope allows DNA properties to be selectively imaged. The substrate on which the DNA is fixed is a silica surface grafted with silanes molecules ended with amine groups.
We investigate the relevance of dynamic quantum coherence in the energy transfer efficiency of molecular aggregates. We contrast the dynamics after excitation of a quantum mechanical system with that of a classical system.
Living cells dynamically modulate the local morphologies of their actin cytoskeletons to perform biological functions, including force transduction, intracellular transport, and cell division. A major challenge is to understand how diverse structures of the actin cytoskeleton are assembled from a limited set of molecu...
A great variety of biologically relevant monolayers present phase coexistence characterized by domains formed by lipids in an ordered phase state dispersed in a continuous, disordered phase. The difference in surface densities between these phases originates inter-domain dipolar interactions, which are relevant for th...
The mutual information between a set of stimuli and the elicited neural responses is compared to the corresponding decoded information. The decoding procedure is presented as an artificial distortion of the joint probabilities between stimuli and responses.
Prion diseases are invariably fatal neurodegenerative diseases that affect humans and animals. Unlike most other amyloid forming neurodegenerative diseases, these can be highly infectious.
Aspects of cell metabolism are modeled by ordinary differential equations describing the change of intracellular chemical concentrations. There is a correspondence between this dynamical system and a complex network.
The field of computational modeling of the brain is advancing so rapidly that now it is possible to model large scale networks representing different brain regions with a high level of biological detail in terms of numbers and synapses. For a theoretician approaching a neurobiological question, it is important to anal...
Directed collective cell migration is central in morphogenesis, wound healing and cancer progression1,2. Although it is well-accepted that the molecular anisotropy of the micro-environment guides this migration3,4, its impact on the pattern of the cell flows remains largely unexplored.
We adopt an operatorial method based on the so-called creation, annihilation and number operators in the description of different systems in which two populations interact and move in a two-dimensional region. In particular, we discuss diffusion processes modeled by a quadratic hamiltonian.
In this work, we propose a structured illumination (SI) method based on a two-photon excitation (TPE) scanning laser beam. Advantages of TPE methods include optical sectioning, low photo-toxicity, and robustness in the face of sample induced scattering.
Bacterial cells exhibit a diverse array of shapes and sizes, largely governed by their cell walls in conjunction with cytoskeletal proteins and internal turgor pressure. The present study develops a theoretical framework for modeling the shape dynamics of actively expanding bacterial cell walls, grounded in the concep...
Controlled deposition of DNA on graphene films obtained with the aid of mechanical splitting of graphite on a substrate with an epoxy sublayer is demonstrated. The DNA molecules are visualized using AFM.
FoF1-ATP synthase is the enzyme that provides the 'chemical energy currency' adenosine triphosphate, ATP, for living cells. The formation of ATP is accomplished by a stepwise internal rotation of subunits within the enzyme.
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 scale under confined and unsteady flow conditions using a combination of microfluid...
So fast is the growth of a culture of E. coli that it led researchers to overlook a possible death rate. As a matter of fact, the experiments done in the first half of the 20th century were unable to detect any mortality.
Reaction coordinates (RCs) are the few essential coordinates of a protein that control its functional processes, such as allostery, enzymatic reaction, and conformational change. They are critical for understanding protein function and provide optimal enhanced sampling of protein conformational changes and states.
We simulate long self-avoiding chains using a weighted-biased sampling Monte-Carlo algorithm, and compute the probabilities for chain looping with and without a protrusion. We find that a protrusion near one of the chain's termini reduces the probability of looping, even for chains much longer than the protrusion-...
Presented with sensory challenges, living cells employ extensive noisy, fluctuating signalling and communication among themselves to compute a physiologically proper response which often results in symmetry breaking. We propose, based on the results of a coupled stochastics oscillators model that biological computatio...
We present a model for host-parasite dynamics which incorporates both vertical and horizontal transmission as well as spatial structure. Our model consists of stacked contact processes (CP), where the dynamics of the host is a simple CP on a lattice while the dynamics of the parasite is a secondary CP which sits on to...
In this work, we study the dynamics of a SEIRS epidemic model with a periodic time-dependent transmission rate. Emphasizing the influence of the seasonality frequency on the system dynamics, we analyze the largest Lyapunov exponent along parameter planes finding large chaotic regions.
This study investigates the radial densification of spruce wood using explicit Finite Element Method simulations, focusing on the effects of various densification protocols. These protocols include quasi-static compression, oscillatory excitation, and self-densification through shrinking hydrogel fillings and their im...
We consider two systems of active swimmers moving close to a solid surface, one being a living population of wild-type \textit{E. coli} and the other being an assembly of self-propelled Au-Pt rods.
Analytical and numerical calculations are presented for the mechanical response of fiber networks in a state of axisymmetric prestress, in the limit where geometric non-linearities such as fiber rotation are negligible. This allows us to focus on the anisotropy deriving purely from the non-linear force-extension curve...
Researches are focused on the elaboration of enzymatic microconductometric device for heavy metal ions detection in water solutions. The manuscript includes a general introduction, the first chapter contains bibliographic review, the second chapter described the fundamentals of conductometric transducers, the third ch...
Approximately 1% of the known protein structures display knotted configurations in their native fold but their function is not understood. It has been speculated that the entanglement may inhibit mechanical protein unfolding or transport, e.g., as in cellular threading or translocation processes through narrow biologi...
An important transition after the origin of life was the first emergence of a Darwinian population, self-reproducing entities exhibiting differential reproduction, phenotypic variation, and inheritance of phenotypic traits. The simplest system we can imagine to have these properties would consist of a compartmentalize...
Calmodulin (CaM) is a ubiquitous calcium binding protein consisting of two structurally similar domains with distinct stabilities, binding affinities, and flexibilities. We present coarse grained simulations that suggest the mechanism for the domain's allosteric transitions between the open and closed conformation...
We report here on the pitfalls of the simulation model introduced in the "Capturing Phase Behavior of Ternary Lipid Mixtures with a Refined Martini Coarse-Grained Force Field" [Journal of Chemical Theory and Computation 2018, 14, 11, 6050-6062]. This refined Martini model was reported to reproduce experimental...
Active microrheology is a valuable tool to determine viscoelastic properties of polymer networks. Observing the beads response to the excitation of a reference leads to dynamic and morphological information of the material.
Photosystems II and I (PSII and PSI) are the reaction centre complexes that drive the light reactions of photosynthesis. PSII performs light-driven water oxidation (quantum efficiencies and catalysis rates of up to 80% and 1000 $e^{-}\text{s}^{-1}$, respectively) and PSI further photo-energises the harvested electrons...
Life in complex systems, such as cities and organisms, comes to a standstill when global coordination of mass, energy, and information flows is disrupted. Global coordination is no less important in single cells, especially in large oocytes and newly formed embryos, which commonly use fast fluid flows for dynamic reor...
Charge diffusion through desoxyribonucleic acid (DNA) is a physico-chemical phenomenon that on the one hand is being explored for technological purposes, on the other hand is applied by nature for various informational processes in life. With regard to the latter, increasing experimental and theoretical evidence indic...
We present a new model for the dynamics of the presynaptic intracellular calcium concentration in neurons evoked by various stimulation protocols. The aim of the model is twofold: We want to discuss the calcium transients during and after specific stimulation protocols as they are used to induce long-term-depression a...
To initiate tumbling of an E. coli, one of the helical flagella reverses its sense of rotation. It then transforms from its normal form first to the transient semicoiled state and subsequently to the curly-I state.
We describe a recent multiscale approach based on the concurrent coupling of constrained molecular dynamics for long biomolecules with a mesoscopic lattice Boltzmann treatment of solvent hydrodynamics. The multiscale approach is based on a simple scheme of exchange of space-time information between the atomistic and m...
Motivated by recent experiments demonstrating that motile algae get trapped in draining foams, we study the trajectories of microorganisms confined in model foam channels (section of a Plateau border). We track single Chlamydomonas reinhardtii cells confined in a thin three-circle microfluidic chamber and show that th...
Babesia microti causes emergency human babesiosis. However, little is known about the alterations in B. microti invaded red blood cells (Bm-RBCs) at the individual cell level.
Here the term "high frequency" refers to daily, weekly or monthly birth data. The fluctuations of daily birth numbers show a succession of spikes and dips which, at least at first sight, looks almost as random as white noise.
Ensilication is a technology we developed that can physically stabilise proteins in silica without use of a pre-formed particle matrix. Stabilisation is done by tailor fitting individual proteins with a silica coat using a modified sol-gel process.
With the number of sequenced genomes now over one hundred, and the availability of rough functional annotations for a substantial proportion of their genes, it has become possible to study the statistics of gene content across genomes. Here I show that, for many high-level functional categories, the number of genes in...
Chemo-mechanical waves on active deformable surfaces are a key component for many vital cellular functions. In particular, these waves play a major role in force generation and long-range signal transmission in cells that dynamically change shape, as encountered during cell division or morphogenesis.
Recent high resolution structures for viral capsids with 12, 32 and 72 subunits ($T1$, $T3$ and $T7$ viruses) have confirmed theoretical predictions of an icosadeltahedral structure with 12 subunits having five nearest neighbors (pentamers) and $(10T+2)-12$ subunits having six nearest neighbor subunits (hexamers). Her...

Subsets and Splits

No community queries yet

The top public SQL queries from the community will appear here once available.