All posts under tag "Quantitative Biology"
The utilization of multiple phosphorylation sites in regulating a biological response is ubiquitous in cell signaling. If each site contributes an additional, equivalent binding site, then one consequence of an increase in the number of phosphorylations may be to increase the probability that, upon
We present a simple algorithm for detecting oscillatory behavior in discrete data. The data is used as an input driving force acting on a set of simulated damped oscillators. By monitoring the energy of the simulated oscillators, we can detect oscillatory behavior in data. In application to in vivo
Molecule-based devices are envisioned to complement silicon devices by providing new functions or already existing functions at a simpler process level and at a lower cost by virtue of their self-organization capabilities, moreover, they are not bound to von Neuman architecture and this may open the
Immune system is the most important defense system to resist human pathogens. In this paper we present an immune model with bipartite graphs theory. We collect data through COPE database and construct an immune cell- mediators network. The act degree distribution of this network is proved to be powe
Background: Human behavior shapes infectious disease dynamics, yet its integration into transmission models remains fragmented. Recent epidemics, particularly COVID-19, highlight the need for models capturing adaptation to perceived risk, social influence, and policy signals. This review synthesizes
In the context of multistability driven diseases, like cancer, spatiotemporal plasticity plays a significant role to achieve a spectrum of phenotypic variations. The interplay between gene regulatory networks and environmental factors, such as resource competition and spatial diffusion, plays a cruc
Bistability of MAP kinase (MAPK) activity has been suggested to contribute to several cellular processes, including differentiation and long-term synaptic potentiation. A recent model (48) predicts bistability due to interactions of the kinases and phosphatases in the MAPK pathway, without feedback
A new strategy with bone tissue engineering by mesenchymal stem cell transplantation on titanium implant has been dawn attention. The surface scaffold properties of titanium surface play an important role in bone regenerative potential of cells. The surface topography and chemistry are postulated to
Single-cell RNA-seq (scRNA-seq) enables atlas-scale profiling of complex tissues, revealing rare lineages and transient states. Yet, assigning biologically valid cell identities remains a bottleneck because markers are tissue- and state-dependent, and novel states lack references. We present CellMas
Biological neural networks (BNNs) are increasingly explored for their rich dynamics, parallelism, and adaptive behavior. Beyond understanding their function as a scientific endeavour, a key focus has been using these biological systems as a novel computing substrate. However, BNNs can only function
Antimicrobial protocols - using substances such as antibiotics or disinfectants - remain the preferred option for preventing the spread of pathogenic bacteria. However, bacteria can develop mechanisms to reduce their antimicrobial susceptibility, which can lead to treatment failure and the selection
We define a notion of coupling time with ambiguities for interacting particle systems, and show how this can be used to prove ergodicity and to bound the convergence time to equilibrium and the decay of correlations at equilibrium. A motivation is to provide simple conditions which ensure that pertu
We calculate analytically the critical connectivity $K_c$ of Random Threshold Networks (RTN) for homogeneous and inhomogeneous thresholds, and confirm the results by numerical simulations. We find a super-linear increase of $K_c$ with the (average) absolute threshold $|h|$, which approaches $K_c(|h|
We demonstrate that a common-line method can assemble a 3D oversampled diffracted intensity distribution suitable for high-resolution structure solution from a set of measured 2D diffraction patterns, as proposed in experiments with an X-ray free electron laser (XFEL) (Neutze {it et al.}, 2000). Eve
The study of the response of complex dynamical social, biological, or technological networks to external perturbations has numerous applications. Random Boolean Networks (RBNs) are commonly used a simple generic model for certain dynamics of complex systems. Traditionally, RBNs are interconnected ra
How do social animals make effective decisions in the absence of a leader? While coordination can improve accuracy, it also introduces delays as information propagates through the group. In changing environments, these delays can outweigh the benefits of globally coordinated decisions, even when loc
Interpretation of animal behavior, especially as cooperative or selfish, is a challenge for evolutionary theory. Strategy of a competition should follow from corresponding Darwinian payoffs for the available behavioral options. The payoffs and decision making processes, however, are difficult to obs
Comparative genomics methods are widely used to aid the functional annotation of non coding DNA regions. However, aligning non coding sequences requires new algorithms and strategies, in order to take into account extensive rearrangements and turnover during evolution. Here we present a novel large
We report the results of our search for power-law electrical signals in the human brain, using subdural electrocorticographic recordings from the surface of the cortex. The power spectral density (PSD) of these signals has the power-law form $ P(f)sim f^{-chi} $ from 80 to 500 Hz. This scaling index
Virus trafficking is fundamental for infection success and plasmid cytosolic trafficking is a key step of gene delivery. Based on the main physical properties of the cellular transport machinery such as microtubules, motor proteins, our goal here is to derive a mathematical model to study cytoplasmi
Regions in the genome that affect complex traits, quantitative trait loci (QTL), can be identified using statistical analysis of genetic and phenotypic data. When restricted maximum-likelihood (REML) models are used, the mapping procedure is normally computationally demanding. We develop a new effic
This review presents the elastic theory of low-dimensional (one- and two-dimensional) continua and its applications in bio- and nano-structures. First, the curve and surface theory, as the geometric representation of the low-dimensional continua, is briefly described through Cartan moving frame meth
Synaptic transmission must balance the need for reliable signalling against the metabolic cost of achieving that reliability. How energetic constraints shape synaptic precision and its regulation during plasticity remains unclear. Here we develop an energy--constrained framework in which synapses mi
In this work we propose a novel algorithmic strategy that allows for an efficient characterization of the whole set of stable fluxes compatible with the metabolic constraints. The algorithm, based on the well-known Bethe approximation, allows the computation in polynomial time of the volume of a non
The effective application of foundation models to translational research in immune-mediated diseases requires multimodal patient-level representations that can capture complex phenotypes emerging from multicellular interactions. Yet most current biological foundation models focus only on single-cell
Social entities only exist in virtue of collective acceptance or recognition, or acknowledgement by two or more individuals in the context of joint activities. Joint activities are made possible by the coordination of plans for action, and the coordination of plans for action is made possible by the
Diversity-Generating Retroelements (DGRs) create rapid, targeted variation within specific genomic regions in phages and bacteria. They operate through stochastic retro-transcription of a template region (TR) into a variable region (VR), which typically encodes ligand-binding proteins. Despite their
We consider a general incompressible finite model protein of size M in its environment, which we represent by a semiflexible copolymer consisting of amino acid residues classified into only two species (H and P, see text) following Lau and Dill. We allow various interactions between chemically unbon
The notion of tissue surface tension has provided a physical understanding of morphogenetic phenomena such as tissue spreading or cell sorting. The measurement of tissue surface tension so far relied on strong approximations on the geometric profile of a spherical droplet compressed between parallel
The free-energy landscape of the alpha-helix of protein G is studied by means of metadynamics coupled with a solute tempering algorithm. Metadynamics allows to overcome large energy barriers, whereas solute tempering improves the sampling with an affordable computational effort. From the sampled fre
We propose a maximum entropy (ME) based approach to smooth noise not only in data but also to noise amplified by second order derivative calculation of the data especially for electroencephalography (EEG) studies. The approach includes two steps, applying method of ME to generate a family of filters
We found theoretically that competition between ~Kq^4 and ~Qq^2 terms in the Fourier transformed conformational energy of a single lipid chain, in combination with inter-chain entropic repulsion in the hydrophobic part of the lipid (bi)layer, may cause a crossover on the bilayer pressure-area isothe
We study a simplified stochastic model for the vascularization of a growing tumor, incorporating the formation of new blood vessels at the tumor periphery as well as their regression in the tumor center. The resulting morphology of the tumor vasculature differs drastically from the original one. We
In contrast to the conventional wisdom that scale-free networks are prone to epidemic propagation, in the paper we present that disease spreading is inhibited in fractal scale-free networks. We first propose a novel network model and show that it simultaneously has the following rich topological pro
Representation of intracellular signaling networks as directed graphs allows for the identification of regulatory motifs. Regulatory motifs are groups of nodes with the same connectivity structure, capable of processing information. The bifan motif, made of two source nodes directly cross-regulating
In this paper, we introduce a gauge-mediated Epidemiological Model inspired by Quantum Electrodynamics (QED). In this model, the ``direct contact'' paradigm of classical SIR models is replaced by a gauge-mediated interaction where the environment, represented by a pathogen field $varphi$, plays a fu
The widespread presence of antibiotic resistance and virulence among Staphylococcus isolates has been attributed to lateral genetic transfer (LGT) between different strains or species. However, there has been very little study of the extent of LGT in Staphylococcus species using a phylogenetic appro
It previously has been discovered that visible light irradiation of crystalline substrates can lead to enhancement of subsequent enzymatic reaction rates as sharply peaked oscillatory functions of irradiation time. The particular activating irradiation times can vary with source of a given enzyme an
3' untranslated regions (3' UTRs) contain binding sites for many regulatory elements, and in particular for microRNAs (miRNAs). The importance of miRNA-mediated post-transcriptional regulation has become increasingly clear in the last few years. We propose two complementary approaches to the stati
Developing fast and efficient algorithms for retrieval of objects to a given user query is an area of active research. The present study investigates retrieval of time series objects from a phoneme database to a given user pattern or query. The proposed method maps the one-dimensional time series re
RNA polymerase (RNAP) is an enzyme that synthesizes a messenger RNA (mRNA) strand which is complementary to a single-stranded DNA template. From the perspective of physicists, an RNAP is a molecular motor that utilizes chemical energy input to move along the track formed by a DNA. In many circumstan
The rules governing cell division and differentiation are central to understanding the mechanisms of development, aging and cancer. By utilising inducible genetic labelling, recent studies have shown that the clonal population in transgenic mouse epidermis can be tracked in vivo. Drawing on these re
Filamentous phage, such as fd used in this study, are thread-shaped bacterial viruses. Their outer coat is a tube formed by thousands equal copies of the major coat protein pVIII. We constructed libraries of random peptides fused to all pVIII domains and selected phages that act as probes specific f
Cooperation plays a key role in the evolution of complex systems. However, the level of cooperation extensively varies with the topology of agent networks in the widely used models of repeated games. Here we show that cooperation remains rather stable by applying the reinforcement learning strategy
Berg and Purcell [Biophys. J. 20, 193 (1977)] calculated how the accuracy of concentration sensing by single-celled organisms is limited by noise from the small number of counted molecules. Here we generalize their results to the sensing of concentration ramps, which is often the biologically releva
We introduce and analyze a waiting time model for the accumulation of genetic changes. The continuous time conjunctive Bayesian network is defined by a partially ordered set of mutations and by the rate of fixation of each mutation. The partial order encodes constraints on the order in which mutatio
Numerical simulations of the behavior of the osteonal structure are more and more acute and an important parameter is the pressure of the bony fluid. Haversian and Volkmann canals contain blood vessels that transport oxygen and nutrients necessary for the cellular activity. The pressure in these ves
On exposure to 1,2-propanediol (1,2-PD), Salmonella enterica serovar Typhimurium LT2 produces 1,2-PD utilization (Pdu) microcompartments (MCPs), nanoscale protein-bound shells that encapsulate metabolic enzymes. MCPs serve as a bioengineering platform to study reaction organization and enhance flux
A model is presented to describe the nucleotide and repeat addition processivity by the telomerase. In the model, the processive nucleotide addition is implemented on the basis of two requirements: One is that stem IV loop stimulates the chemical reaction of nucleotide incorporation, and the other o
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
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