OpenWorm is an international collaboration with the aim of understanding how behavior Caenorhabditis elegans (C. elegans) emerges from its underlying physiological processes. The project has developed a modular simulation engine to create computational models worm. modularity makes it possible easily modify model, incorporate new experimental data and test hypotheses. modeling framework incorporates both biophysical neuronal simulations novel fluid-dynamics-based soft-tissue for physical...

SARS-CoV-2 is a virus for which an outstanding number of genome variants were collected, sequenced and stored from sources all around the world. Raw data in FASTA format include 16.8 million genomes, each ≈29,900 nt (nu­cleotides), with total size ≈500 ∙ 10 9 nt, or 465 Gb. We suggest approach to representation organization, this can be losslessly operative memory (RAM) common PC. Moreover, just ≈330 Mb will enough. Aligning genomes versus initial Wuhan-Hu-1 reference sequence allows...

The translation start site plays an important role in the control of efficiency eukaryotic mRNAs. recognition AUG codon by ribosomes is considered to depend on its nucleotide context. However, fraction mRNAs with a suboptimal context relatively large. It may be expected that mRNA should possess some features providing efficient translation, including proper site. has been experimentally shown downstream hairpin located certain positions respect can compensate part for and also increases from...

The nematode C. elegans is the only animal with a known neuronal wiring diagram, or "connectome". During last three decades, extensive studies of have provided wide-ranging data about it, but few systematic ways integrating thes

To better understand how a nervous system controls the movements of an organism, we have created three-dimensional computational biomechanical model Caenorhabditis elegans body based on real anatomical structure. The is with particle system-based simulation engine known as Sibernetic, which implements smoothed particle-hydrodynamics algorithm. includes elastic body-wall cuticle subject to hydrostatic pressure. This then driven by muscle cells that contract and relax, whose positions shape...

The comparison of the development SARS-CoV-2 epidemic in several neighboring regions can help researchers to assess risks and develop more effective strategies approaches field preventive medicine. We analyzed infection mortality statistics for 2020–2022 period ten individual Siberian Federal District Russia. also sequenced complete genomes, which allowed us analyze genetic diversity circulated each build a phylogenetic dendrogram virus variants. ParSeq v.1.0 software was developed automate...

A hydrodynamic description of protein folding is proposed and illustrated with a lattice model, which has free energy surface (FES) typical proteins two-state kinetics. The flows from the unfolded to native state are concentrated in limited region FES. rest occupied by flow ``vortex'', does not lead state. In contrast intermediates that associated local minima, vortex visible on interpretation thus provides new insights into mechanism can be useful complement standard analyses.

How does the brain process sensory stimuli, and decide whether to initiate locomotor behaviour? To investigate this question we develop two whole body computer models of a tadpole. The "Central Nervous System" (CNS) model uses evidence from whole-cell recording define 2300 neurons in 12 classes study how signals skin stop swimming. In response stimulation, it generates realistic pathway spiking shows hindbrain memory populations on each side can compete reticulospinal neuron firing start 3-D...

We have designed a model lattice protein that has two stable folded states, the lower free energy native state and latent of somewhat higher energy. The states sizable part their structures in common (two "α-helices") differ content "α-helices" "β-strands" rest structures; i.e. for state, this is α-helical, it composed β-strands. Thus, surface mimics amyloidogenic proteins form well organized fibrils under appropriate conditions. A Gō-like potential was used folding process simulated with...

The nematode C. elegans is historically one of the most studied model organism in biology and only to have its full connectome mapped. OpenWorm [1] a project dedicated recreating as virtual computer. takes an Open Science approach development, relying on volunteer contributions making all code, data documentation publicly available at time production. has two long term goals. first functionally reproduce behaviour wild-type variety environmental contexts, extent that simulated statistically...

The coronavirus pandemic caused by the SARS-CoV-2 virus, which humanity resisted using latest advances in science, left behind, among other things, extensive genetic data. Every day since end of 2019, samples virus genomes have been collected around world, makes it possible to trace its evolution detail from emergence present. accumulated statistics testing results showed that number confirmed cases infection was at least 767.5 million (9.5 % current world population, excluding asymptomatic...

OpenWorm is an international collaboration with the aim of producing integrative computational model Caenorhabditis elegans to further understanding how macroscopic behaviour organism emerges from aggregated biophysical processes. A core component project involves integration electrophysiological modelling and predictive-corrective incompressible smoothed particle hydrodynamics (PCISPH) neuronal muscle dynamics effect nematode’s behaviour. Several tools are being utilised developed in course project:

The article presents an efficient multithreaded implementation of the modern 3SEQ algorithm for detecting recombinant genetic sequences, tested on viral genomes. work was carried out within framework project to create a domestic (Russian) web-platform (bioprojects.iis.nsk.su) solving wide range problems related data analysis in field bioinformatics, virology and epidemiology. A genome emerges when two different variants virus genomes same species exchange their parts, which is possible case...

A brief description of the multi-level model quark-gluon media is presented. In terms this model, we use Wigner–Segal approach to elementary particles and modify Han–Nambu scheme. By doing so, suggest view proton’s electric charge as a special case color charges quarks. While fractional quarks are interpreted statistical averages integer charges.

Development of computer models imitating the work nervous systems living organisms, taking into account their morphology and electrophysiology, is one important promising branches computational neurobiology. It often sought to model not only system, but also body, muscles, sensory systems, a virtual three-dimensional physical environment in which behavior an organism can be observed provides its with adequate data streams that change response movement organism. For system hundreds or...

One of the current problems at interface between neuroscience, biophysics, and computational modeling is reverse-engineering reproduction Caenorhabditis elegans using computer simulation. The aim our research was to develop models techniques for solving this problem while participating in international open science OpenWorm Project. We have suggested a typical C. neuron pharyngeal muscle cell, which were constructed optimized NEURON simulation environment. available experimental data about...

The Multi-Level Model (=MLM) was suggested by A. Levichev as a description of quarks and gluons. review recalls MLM-terminology while MLM-findings (for leptons) are compared to the theoretical experimental data accepted Standard (=SM). MLM is based on Segal’s compact space-time U(2) sequence embeddings: into U(3), U(4), etc. These groups were called levels (of matter): - 0th (that is, our mundane world), U(3) 1st, U(4) 2nd, Such convention matches SM-quarks' generations list. Each...

A certain class K of GR homogeneous spacetimes is considered. For each pair E, from K, where conformal transformation g . Each E (being or its double cover, as a manifold) interpreted related to an observer in Segal’s universal cosmos. The definition separation d between and based on the integration factor g. carried out separately over region no less than 1 (or greater 1). Certain properties are proven; examples considered; possible directions further research indicated.