Related papers: Study on Antibody-Virus Interaction using Molecula…
The use of oncolytic viruses as cancer treatment has received considerable attention in recent years, however the spatial dynamics of this viral infection is still poorly understood. We present here a stochastic agent-based model describing…
All atom molecular dynamics simulations with explicit water were done to study the interaction between two parallel double-stranded DNA molecules in the presence of the multivalent counterions putrescine (2+), spermidine (3+), spermine (4+)…
The mechanisms of physical and chemical interactions of low temperature plasmas with surfaces can be fruitfully explored using molecular dynamics (MD) simulations. MD simulations follow the detailed motion of sets of interacting atoms…
Human Papillomavirus infection is the most common sexually transmitted infection, and causes serious complications such as cervical cancer in vulnerable female populations in regions such as East Africa. Due to the scarcity of empirical…
Peripheral membrane proteins can reversibly and specifically bind to biological membranes to carry out functions such as cell signalling, enzymatic activity, or membrane remodelling. Structures of these proteins and of their lipid-binding…
The use of ad-hoc engineered viruses in the fight against tumours is one of the greatest ideas in cancer therapeutics within the last three decades. Together with other strategies such as immunotherapies, nanoparticles and adjunct…
The hydrogen peroxide is present in the living cell at small concentrations that increase under the action of the heavy ion beams in the process of anticancer therapy. The interactions of hydrogen peroxide with DNA, proteins and other…
One of the mechanisms that ensure cancer robustness is tumor heterogeneity, and its effects on tumor cells dynamics have to be taken into account when studying cancer progression. There is no unifying theoretical framework in mathematical…
The dynamics of H atom recombination on materials of interest for a EUV lithographer was studied under a longterm low-pressure H2 plasma exposure. The similarity of the experimental plasma with the typical EUV-induced plasma over the…
Antimicrobial peptides (AMPs) play important roles in cancer, autoimmune diseases, and aging. A critical aspect of AMP functionality is their targeted interaction with pathogen membranes, which often possess altered lipid compositions.…
The interface between hemoglobin (Hb) and its environment, in particular water, is of great physiological relevance. Here, results from {\it in vitro}, {\it in vivo}, and computational experiments (molecular dynamics simulations) are…
Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly…
In the tumour microenvironment, cancer cells directly interact with both the immune system and the stroma. It is firmly established that the immune system, historically believed to be a major part of the body's defence against tumour…
Tumor-immune interactions are central to cancer progression and treatment outcomes. In this study, we present a stochastic agent-based model that integrates cellular heterogeneity, spatial cell-cell interactions, and drug resistance…
We develop a Bayesian statistical model and estimation methodology based on Forward Projection Adaptive Markov chain Monte Carlo in order to perform the calibration of a high-dimensional non-linear system of Ordinary Differential Equations…
A mathematical model for the quantitative analysis of cancer immune interaction, considering the role of antibodies has been proposed in this paper. The model is based on the clinical evidence, which states that antibodies can directly kill…
Predicting how protein mutations affect drug binding remains a major challenge, particularly when the mutations are distal from the binding site. In this study, we introduce a coupled simulation workflow that combines long-time-scale…
Equipment sharing among people who inject drugs (PWID) is a key risk factor in infection by hepatitis C virus (HCV). Both the effectiveness and cost-effectiveness of interventions aimed at reducing HCV transmission in this population (such…
Antibodies play an essential role in the immune response to viral infections, vaccination, or antibody therapy. Nevertheless, they can be either protective or harmful during the immune response. Moreover, competition or cooperation between…
Drug resistance to HIV-1 Protease involves accumulation of multiple mutations in the protein. Here we investigate the role of these mutations by using molecular dynamics simulations which exploit the influence of the native-state topology…