scholarly journals Agent-based Models for Detecting the Driving Forces of Biomolecular Interactions

2021 ◽  
Author(s):  
Stefano Maestri ◽  
Emanuela Merelli ◽  
Marco Pettini
Keyword(s):  
In Silico ◽  
Autonomous Agents ◽  
High Efficiency ◽  
Driving Forces ◽  
Agent Based ◽  
Biochemical Processes ◽  
Agent Based Modelling ◽  
Electrodynamic Forces ◽  
Shed Light

Abstract Agent-based modelling and simulation have been effectively applied to the study of complex biological systems, especially when composed by a large number of interacting entities. Representing biomolecules as autonomous agents allows this approach to bring out the global behaviour of biochemical processes as resulting from local molecular interactions. In this paper, we leverage the capabilities of the agent paradigm to construct an in silico replica of the glycolytic pathway of baker’s yeasts; the aim is to detect the role that long-range electrodynamic forces might have on the rate of glucose oxidation. Experimental evidences have shown that random encounters and short-range potentials might not be sufficient to explain the high efficiency of biochemical reactions in living cells. However, while the latest in vitro studies are limited by the present-day technology, agent-based simulations provide an in silico support to the outcomes hitherto obtained and shed light on behaviours not yet well understood. Our results reveal to be able to grasp properties hard to uncover through other computational methods, such as the effect of electromagnetic potentials on glycolytic oscillations.

scholarly journals Isolation, Characterization, and Agent-Based Modeling of Mesenchymal Stem Cells in a Bio-construct for Myocardial Regeneration Scaffold Design

Data ◽  
2019 ◽  
Vol 4 (2) ◽  
pp. 71 ◽  
Author(s):  
Diana Victoria Ramírez López ◽  
María Isabel Melo Escobar ◽  
Carlos A. Peña-Reyes ◽  
Álvaro J. Rojas Arciniegas ◽  
Paola Andrea Neuta Arciniegas
Keyword(s):  
Stem Cells ◽  
Mesenchymal Stem Cells ◽  
In Silico ◽  
Cardiac Tissue ◽  
Cellular Level ◽  
Cell Behavior ◽  
Agent Based Model ◽  
Agent Based ◽  
And Migration

Regenerative medicine involves methods to control and modify normal tissue repair processes. Polymer and cell constructs are under research to create tissue that replaces the affected area in cardiac tissue after myocardial infarction (MI). The aim of the present study is to evaluate the behavior of differentiated and undifferentiated mesenchymal stem cells (MSCs) in vitro and in silico and to compare the results that both offer when it comes to the design process of biodevices for the treatment of infarcted myocardium in biomodels. To assess in vitro behavior, MSCs are isolated from rat bone marrow and seeded undifferentiated and differentiated in multiple scaffolds of a gelled biomaterial. Subsequently, cell behavior is evaluated by trypan blue and fluorescence microscopy, which showed that the cells presented high viability and low cell migration in the biomaterial. An agent-based model intended to reproduce as closely as possible the behavior of individual MSCs by simulating cellular-level processes was developed, where the in vitro results are used to identify parameters in the agent-based model that is developed, and which simulates cellular-level processes: Apoptosis, differentiation, proliferation, and migration. Thanks to the results obtained, suggestions for good results in the design and fabrication of the proposed scaffolds and how an agent-based model can be helpful for testing hypothesis are presented in the discussion. It is concluded that assessment of cell behavior through the observation of viability, proliferation, migration, inflammation reduction, and spatial composition in vitro and in silico, represents an appropriate strategy for scaffold engineering.

Performance of a Parallel Multi-Agent Simulation using Graphics Hardware

2014 ◽  
Vol 6 (4) ◽  
pp. 72-91
Author(s):  
Timothy W. C. Johnson ◽  
John R. Rankin
Keyword(s):  
Large Scale ◽  
Autonomous Agents ◽  
Graphics Hardware ◽  
Processing Unit ◽  
Agent Based ◽  
Agent Based Modelling ◽  
Processing Power ◽  
Agent Simulation ◽  
Multi Agent ◽  
Graphical Processing

Large-scale Agent-Based Modelling and Simulation (ABMS) is a field of research that is becoming increasingly popular as researchers work to construct simulations at a higher level of complexity and realism than previously done. These systems can not only be difficult and time consuming to implement, but can also be constrained in their scope due to issues arising from a shortage of available processing power. This work simultaneously presents solutions to these two problems by demonstrating a model for ABMS that allows a developer to design their own simulation, which is then automatically converted into code capable of running on a mainstream Graphical Processing Unit (GPU). By harnessing the extra processing power afforded by the GPU this paper creates simulations that are capable of running in real-time with more autonomous agents than allowed by systems using traditional x86 processors.

scholarly journals A new primer for metabarcoding of spider gut contents

2019 ◽  
Author(s):  
Denis Lafage ◽  
Vasco Elbrecht ◽  
Jordan Cuff ◽  
Dirk Steinke ◽  
Peter Hambäck ◽  
...  
Keyword(s):  
Related Species ◽  
In Silico ◽  
High Efficiency ◽  
New Technologies ◽  
Prey Species ◽  
Carabid Beetles ◽  
Gut Contents ◽  
Malaise Trap ◽  
Closely Related Species

As a key predator group, spiders have received a lot of attention by food web ecologists in diverse fields such as pest control, pollutant transfers, and cross-ecosystem fluxes. The difficulty involved in studying their diet has led to the use of new technologies such as metabarcoding of gut contents. The amplification of a broad range of spider prey without amplifying spiders themselves is challenging and, until now, an efficient universal primer purposed for this has not existed. We developed a novel forward primer (NoSpi2) targeting the cytochrome c oxidase subunit I gene. The primer was designed not to amplify spiders of the oval calamistrum clade (Lycosidae and closely related species) while still amplifying most other invertebrates. NoSpi2 was tested together with the reverse primer BR2 in silico, in vitro on single specimens of prey and spiders, on mock and malaise trap communities, and in an ecological application. In silico evaluation predicted high primer bias for spiders of the oval calamistrum clade and low bias for all other invertebrates. These results were largely confirmed by in vitro tests. Additionally, some spider families were not amplified contrary to our expectations. We demonstrated a high efficiency for the primer pair NoSpi2/BR2 which recovered up to 94% of taxa in the mock community and 85% of the taxa detected by the best invertebrate primer pair known (BF3+BR2) for the malaise trap community. The field experiment showed that Lycosidae spider DNA is not amplified by the NoSpi2 primer set. It also demonstrated a broad range of detectable prey species. We found prey from 12 orders, 67 families and 117 species. The ability of the NoSpi2/BR2 primer combination to reliably amplify prey species, without amplifying any predator reads, makes it an ideal choice for gut-content analysis for spider species of lycosids and closely related species, even enabling the homogenization of entire spider specimens without dissection. Given that the detected prey species included other spiders and carabid beetles, this primer could be used for not only diet and biological control studies, but also to study intra-guild predation.

scholarly journals Host-Directed FDA-Approved Drugs with Antiviral Activity against SARS-CoV-2 Identified by Hierarchical In Silico/In Vitro Screening Methods

2021 ◽  
Vol 14 (4) ◽  
pp. 332
Author(s):  
Tiziana Ginex ◽  
Urtzi Garaigorta ◽  
David Ramírez ◽  
Victoria Castro ◽  
Vanesa Nozal ◽  
...  
Keyword(s):  
Antiviral Activity ◽  
Viral Entry ◽  
In Silico ◽  
Screening Methods ◽  
Speed Up ◽  
Approved Drugs ◽  
Fda Approved Drugs ◽  
Shed Light ◽  
Virtual Screening Approach

The unprecedent situation generated by the COVID-19 global emergency has prompted us to actively work to fight against this pandemic by searching for repurposable agents among FDA approved drugs to shed light into immediate opportunities for the treatment of COVID-19 patients. In the attempt to proceed toward a proper rationalization of the search for new antivirals among approved drugs, we carried out a hierarchical in silico/in vitro protocol which successfully combines virtual and biological screening to speed up the identification of host-directed therapies against COVID-19 in an effective way. To this end a multi-target virtual screening approach focused on host-based targets related to viral entry, followed by the experimental evaluation of the antiviral activity of selected compounds, has been carried out. As a result, five different potentially repurposable drugs interfering with viral entry—cepharantine, clofazimine, metergoline, imatinib and efloxate—have been identified.

scholarly journals OBTAINING HIGH-QUALITY PLANTING MATERIAL OF FOREST BERRY PLANTS BY CLONAL MICROPROPAGATION FOR RESTORATION OF CUTOVER PEATLANDS

2021 ◽  
pp. 21-29
Author(s):  
Sergey Makarov ◽  
◽  
Irina Kuznetsova ◽  
Anton Chudetsky ◽  
Sergey Rodin ◽  
...  
Keyword(s):  
High Efficiency ◽  
Sharp Decrease ◽  
Environmental Damage ◽  
Agent Based ◽  
Clonal Micropropagation ◽  
Planting Material ◽  
Mercuric Chloride Solution ◽  
Regenerated Plants ◽  
Berry Crops

The results of studies on the improvement of technology for producing highquality planting material of half-high blueberry and Arctic bramble by the method of clonal micropropagation are presented in the current paper. Creation of forest berry plantations in peat extraction areas allows reducing environmental damage and significantly increasing the efficiency of the timber industry. In recent decades, there has been an increasing interest in the creation of forest berry plantations on drained and cutover peatlands in Russia and other countries. It is necessary to use varietal planting material for the successful cultivation of forest berry plants on an industrial scale. Clonal micropropagation is the most effective of the vegetative methods for obtaining planting material, which allows receiving a huge amount of healthy planting material all year round in the conditions of a small laboratory area. Chloride-free ecosterilizer and bleaching agent based on sodium hypochlorite “Belizna” with an exposure of 15 and 20 min showed high efficiency in sterilization of explants of half-high blueberry and Arctic bramble. The highest viability of explants of the studied forest berry crops was observed when sterilized with a 0.1 % mercuric chloride solution and 15 min exposure, and its sharp decrease at 20 min exposure. At the stage of micropropagation, with an increase in the concentration of cytokinin 6-BAP from 0.5 to 1.0 mg/L on the nutrient Woody Plant Medium the number of shoots in regenerated plants of half-high blueberry (Northcountry and Northblue cultivars) and Arctic bramble (Anna and Sofia cultivars) increased. The effect of the concentration of IBA-derived auxin on the number and length of roots of regenerated plants was observed at the in vitro rooting stage.

scholarly journals In silico analysis of interaction of compounds, containing photoactivatable groups,with human CYP7 enzymes

2020 ◽  
Vol 64 (5) ◽  
pp. 558-566
Author(s):  
Ya. U. Dzichenka ◽  
M. S. Horetski ◽  
Ya. V. Faletrov ◽  
A. V. Yantsevich ◽  
V. M. Shkumatov ◽  
...  
Keyword(s):  
In Silico ◽  
Binding Mode ◽  
Amino Acid Residues ◽  
Structural Peculiarities ◽  
Close Proximity ◽  
Mechanism Of Interaction ◽  
Covalent Adducts ◽  
Steroid Hydroxylases ◽  
Shed Light

In silico analysis of “protein-ligand” complexes of human CYP7 enzymes with modified borondipyrrome-tene (BODIPY) and steroids, containing photo-activated crosslinking groups, wasperformed in order to identify structural peculiarities of their interaction. It was found that BODIPY molecules and DHEA derivative with diazirine group are able to bind tightly with human steroid-hydroxylases. Binding affinity is comparable with corresponding values for essential ligands of the enzymes. Binding mode of the modified steroid corresponds to the binding mode of essential CYP7 ligands, so formation of hydroxylated products is possible. It was found that presence of both diazirine and NBD groups in a molecule significantly increases affinity of the compound in case of CYP7A1 and, especially, CYP7B1. Amino acid residues, located in a close proximity with photo-activated groups were detected, that can form covalent adducts with them. The obtained results can shed light on the mechanism of interaction of the compounds with recombinant human CYP7 enzymes in vitro. The results can also be used for the identification of modified amino acids of the proteins that are formed under photoactivation of the compounds in vitro.

Mathematical modelling of cell migration

2019 ◽  
Vol 63 (5) ◽  
pp. 631-637
Author(s):  
George Butler ◽  
Jonathan Rudge ◽  
Philip R. Dash
Keyword(s):  
Cell Migration ◽  
Differential Equations ◽  
Mathematical Modelling ◽  
Chemokine Receptor ◽  
Experimental Work ◽  
In Silico ◽  
Agent Based ◽  
Agent Based Modelling ◽  
Receptor Signalling ◽  
Use Of Models

Abstract The complexity of biological systems creates challenges for fully understanding their behaviour. This is particularly true for cell migration which requires the co-ordinated activity of hundreds of individual components within cells. Mathematical modelling can help understand these complex systems by breaking the system into discrete steps which can then be interrogated in silico. In this review, we highlight scenarios in cell migration where mathematical modelling can be applied and discuss what types of modelling are most suited. Almost any aspect of cell migration is amenable to mathematical modelling from the modelling of intracellular processes such as chemokine receptor signalling and actin filament branching to larger scale processes such as the movement of individual cells or populations of cells through their environment. Two common ways of approaching this modelling are the use of models based on differential equations or agent-based modelling. The application of both these approaches to cell migration are discussed with specific examples along with common software tools to facilitate the process for non-mathematicians. We also highlight the challenges of modelling cell migration and the need for rigorous experimental work to effectively parameterise a model.

scholarly journals In Silico Modeling of Biofilm Formation by Nontypeable Haemophilus influenzae In Vivo

mSphere ◽  
2019 ◽  
Vol 4 (4) ◽  
Author(s):  
Jonathan R. Brown ◽  
Joseph Jurcisek ◽  
Vinal Lakhani ◽  
Ali Snedden ◽  
William C. Ray ◽  
...  
Keyword(s):  
Haemophilus Influenzae ◽  
In Silico ◽  
Biofilm Formation ◽  
Host Responses ◽  
Model Parameters ◽  
Agent Based Model ◽  
Content Type ◽  
Agent Based

ABSTRACT Biofilms formed by nontypeable Haemophilus influenzae (NTHI) bacteria play an important role in multiple respiratory tract diseases. Visual inspection of the morphology of biofilms formed during chronic infections shows distinct differences from biofilms formed in vitro. To better understand these differences, we analyzed images of NTHI biofilms formed in the middle ears of Chinchilla lanigera and developed an in silico agent-based model of the formation of NTHI biofilms in vivo. We found that, as in vitro, NTHI bacteria are organized in self-similar patterns; however, the sizes of NTHI clusters in vivo are more than 10-fold smaller than their in vitro counterparts. The agent-based model reproduced these patterns and suggested that smaller clusters occur due to elimination of planktonic NTHI cells by the host responses. Estimation of model parameters by fitting simulation results to imaging data showed that the effects of several processes in the model change during the course of the infection. IMPORTANCE Multiple respiratory illnesses are associated with formation of biofilms within the human airway by NTHI. However, a substantial amount of our understanding of the mechanisms that underlie NTHI biofilm formation is obtained from in vitro studies. Our in silico model that describes biofilm formation by NTHI within the middle ears of Chinchilla lanigera will help isolate processes potentially responsible for the differences between the morphologies of biofilms formed in vivo versus those formed in vitro. Thus, the in silico model can be used to glean mechanisms that underlie biofilm formation in vivo and connect those mechanisms to those obtained from in vitro experiments. The in silico model developed here can be extended to investigate potential roles of specific host responses (e.g., mucociliary clearance) on NTHI biofilm formation in vivo. The developed computational tools can also be used to analyze and describe biofilm formation by other bacterial species in vivo.

scholarly journals An agent based modelling approach to study lockdown efficacy for infectious disease spreads

2020 ◽  
Author(s):  
Anagh Pathak ◽  
Varun Madan Mohan ◽  
Arpan Banerjee
Keyword(s):  
Social Network ◽  
Autonomous Agents ◽  
Local Population ◽  
Small World ◽  
Agent Based ◽  
Scale Free ◽  
Agent Based Modelling ◽  
Spreading Dynamics ◽  
Agent Interaction ◽  
Medical Infrastructure

AbstractWe sought to simulate lockdown scenarios using an Agent Based Modelling (ABM) strategy, which is a new modelling paradigm that seeks to simulate the actions and interactions of autonomous agents within an environment. The spread of infectious viral diseases occur over a connected social network. Specifically, the goal was to understand the effect of network topology and lockdown strategies on disease spreading dynamics. To explore the effect of topology we assumed the social network over which the disease spreads to have small-world or scale-free properties characterized by a rewiring probability and degree distribution respectively. Lockdowns were simulated as intervention strategies that modified the spreading dynamics of infection over a given graph structure through changes in properties of agent interaction. Lockdown efficacy was assessed by the maximum number of infections recorded during a simulation run. Thereafter, lockdown efficacy was evaluated as a function of lockdown start times and duration. Thus, we propose that ABM approach can be used to assess various lockdown strategies that aim to prevent breakdown of medical infrastructure while accounting for realistic social network configurations specific to a local population.Notation

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