We develop a workflow, implemented as a plugin to the molecular visualization program VMD, that can fix ring penetrations with minimal user input. LongBondEliminator, detects ring piercing artifacts by the long, strained bonds that are the local mini...
The crowded interior of a living cell makes performing experiments on simpler in vitro systems attractive. Although these reveal interesting phenomena, their biological relevance can be questionable. A topical example is the phase separation of intri...
The statistical mechanics-based 3-dimensional reference interaction site model with the Kovalenko-Hirata closure (3D-RISM-KH) molecular solvation theory has proven to be an essential part of a multiscale modeling framework, covering a vast region of...
The understanding of interactions between nanomaterials and biological molecules is of primary importance for biomedical applications of nanomaterials, as well as for the evaluation of their possible toxic effects. Here, we carried out extensive mole...
Phospholipid membranes surround the cell and its internal organelles, and their multicomponent nature allows the formation of domains that are important in cellular signalling, the immune system, and bacterial infection. Cytoplasmic compartments are...
Arginine plays a critical role in biomolecular interactions due to its guanidinium side chain, which enables multivalent electrostatic and hydrogen bonding contacts. In this study, atomistic molecular dynamics simulations were conducted across a broa...
Elucidating amyloid formation inside biomolecular condensates requires models that resolve (i) local, chemistry specific contacts controlling β registry and (ii) mesoscale phase behavior and cluster coalescence on microsecond timescales—capabilities...
The SARS-CoV-2 Delta variant is emerging as a globally dominant strain. Its rapid spread and high infection rate are attributed to a mutation in the spike protein of SARS-CoV-2 allowing for the virus to invade human cells much faster and with an incr...
Pharmacogenomics aims to reveal variants associated with drug response phenotypes. Genes whose roles involve the absorption, distribution, metabolism, and excretion of drugs, are highly polymorphic between populations. High coverage whole genome sequ...
Antibiotics are important drugs for the treatment of microbial infections and related diseases. However, due to the abuse of antibiotics, drug resistance has become a serious and urgent problem. The development of new antibiotics is a crucial area of...
Staphylococcus protein A (SpA) is found in the cell wall of Staphylococcus aureus bacteria. Its ability to bind to the constant Fc regions of antibodies means it is useful for antibody extraction, and further integration with inorganic materials can...
Solvents represent the quiet majority in biomolecular systems, yet modeling their influence with both speed and ri:gor remains a central challenge. This study maps the state of the art in implicit solvent theory and practice, spanning classical conti...
Macrolide antibiotics are macrocyclic compounds that are clinically used and prescribed for the treatment of upper and lower respiratory tract infections. They inhibit the synthesis of bacterial proteins by reversible binding to the 23S rRNA at or ne...
Simulation of atomic force microscopy (AFM) computationally emulates experimental scanning of a biomolecular structure to produce topographic images that can be correlated with measured images. Its application to the enormous amount of available high...
The big data concept is currently revolutionizing several fields of science including drug discovery and development. While opening up new perspectives for better drug design and related strategies, big data analysis strongly challenges our current a...
We report on a nanoparticle-based biosensor that represents a label-free homogeneous bioassay suitable for in-vitro biomolecular diagnostics. The underlying detection principle is based on the optical observation of the rotational dynamics of multico...
Current research focuses on a better understanding of the origin of biomolecular asymmetry by the identification and detection of the possibly first chiral molecules that were involved in the appearance and evolution of life on Earth. We have reasons...
Many intrinsically disordered proteins (IDPs) are known to undergo liquid–liquid phase separation (LLPS), which is a physical process that drives the formation of biomolecular condensates and membraneless organelles in biological cells. Molecul...
Epigenetic readout of the combinatorial posttranslational modification comprised of trimethyllysine and asymmetric dimethylarginine (H3K4me3R8me2a) takes place via biomolecular recognition of tandem Tudor-domain-containing protein Spindlin1. Through...
Gaining a fundamental insight into the biomolecular recognition of posttranslationally modified histones by epigenetic reader proteins is of crucial importance to understanding the regulation of the activity of human genes. Here, we seek to establish...
This paper presents a novel Double Buried-Window Junctionless Field-Effect Transistor (DBW-FET) designed for high-sensitivity, label-free biosensing applications. The proposed device integrates two buried windows, one N-type and one P-type, beneath t...
Living organisms are constructed from proteins that assemble into biomolecular complexes, each with a unique shape and function. Our knowledge about the structure–activity relationship of these complexes is still limited, mainly because of thei...
Liquid–liquid phase separation (LLPS) of RNA drives the formation of membraneless organelles, and its dysregulation is closely linked to major human diseases, including cancer, neurodegenerative disorders, and various rare genetic diseases. Cur...
The cellular functions are executed by biological macromolecular complexes in nonequilibrium dynamic processes, which exhibit a vast diversity of conformational states. Solving the conformational continuum of important biomolecular complexes at the a...
Computer modeling of very large biomolecular systems, such as long DNA polyelectrolytes or protein-DNA complex-like chromatin cannot reach all-atom resolution in a foreseeable future and this necessitates the development of coarse-grained (CG) approx...
Molecular dynamics (MD) simulations allow the investigation of the structural dynamics of biomolecular systems with unrivaled time and space resolution. However, in order to compensate for the inaccuracies of the utilized empirical force fields, it i...
Finite element method analysis was applied to the characterization of the biomolecular interactions taking place in a microfluidic assisted microarray. Numerical simulations have been used for the optimization of geometrical and physical parameters o...
Molecular dynamics (MD) simulations are powerful theoretical methods that can reveal biomolecular properties, such as structure, fluctuations, and ligand binding, at the level of atomic detail. In this review article, recent MD simulation studies on...
Gallium nitride (GaN) high-electron-mobility transistor (HEMT) biosensors have recently emerged as promising platforms for highly sensitive and label-free detection of biomolecules. Their exceptional electrical properties, including high carrier mobi...
Biomolecular materials offer tremendous potential for the development of memristive devices due to their low cost of production, environmental friendliness, and, most notably, biocompatibility. Herein, biocompatible memristive devices based on amyloi...
DNA molecular machines have great potential for use in computing systems. Since Adleman originally introduced the concept of DNA computing through his use of DNA strands to solve a Hamiltonian path problem, a range of DNA-based computing elements hav...
Helical polymer bundles are an important fixture in biomolecular systems. The particular structural geometry of helix bundles is dependent on many factors including the length of the polymer chain. In this study, we performed Monte Carlo simulations...
Estimating confidence intervals in small or noisy datasets is a recurring challenge in biomolecular research, particularly when data contain outliers or exhibit high variability. This study introduces a robust statistical method that combines a hybri...
For the progress of point-of-care medicine, where individual health status can be easily and quickly monitored using a handheld sensor, saliva serves as one of the best-suited body fluids thanks to its availability and abundance of physiological indi...
Label-free biomolecular sensors have been widely studied due to their simple operation. L-shaped tunneling field-effect transistors (LTFETs) are used in biosensors due to their low subthreshold swing, off-state current, and power consumption. In a di...
Biomolecular condensates, which assemble via the process of liquid–liquid phase separation (LLPS), are multicomponent compartments found ubiquitously inside cells. Experiments and simulations have shown that biomolecular condensates with many compone...
Particle plasmon resonance (PPR), or localized surface plasmon resonance (LSPR), utilizes intrinsic resonance in metal nanoparticles for sensor fabrication. While diffraction grating waveguides monitor bioaffinity adsorption with out-of-plane illumin...
Rare tautomeric forms of nucleobases can lead to Watson–Crick-like (WC-like) mispairs in DNA, but the process of proton transfer is fast and difficult to detect experimentally. NMR studies show evidence for the existence of short-time WC-like g...
Membrane computing, and more specifically P systems, has been a useful tool in the simulation of biological systems, both at the biomolecular and cellular levels, and also in microbial and ecological communities. The need for greater realism in the s...
Tumor necrosis factor-α (TNF-α) is a drug target in rheumatoid arthritis and several other auto-immune disorders. TNF-α binds with TNF receptors (TNFR), located on the surface of several immunological cells to exert its effect. Hence, the use of inhi...
Maintaining a proper balance between specific intermolecular interactions and non-specific solvent interactions is of critical importance in molecular simulations, especially when predicting binding affinities or reaction rates in the condensed phase...
Concentration gradient generation plays a pivotal role in advancing applications across drug screening, chemical synthesis, and biomolecular studies, yet conventional methods remain constrained by labor-intensive workflows, limited throughput, and in...
Terahertz (THz) fingerprint spectroscopy enables label-free identification of molecular vibrational signatures, but trace biomolecular absorption is too weak to be reliably resolved in free-space measurements. To address this limitation, we propose a...
Morphogenetic modelling and simulation help to understand the processes by which the form and shapes of organs (organogenesis) and organisms (embryogenesis) emerge. This requires two mutually coupled entities: the biomolecular signalling network and...
Biomolecular systems that can process information are sought for computational applications, because of their potential for parallelism and miniaturization and because their biocompatibility also makes them suitable for future biomedical applications...
Estimation of solvent entropy from equilibrium molecular dynamics simulations is a long-standing problem in statistical mechanics. In recent years, methods that estimate entropy using k-th nearest neighbours (kNN) have been applied to internal degree...
Solid surfaces have been shown to affect the aggregation and assembly of many biomolecular systems. One important example is the formation of protein fibrils, which can occur on a range of biological and synthetic surfaces. The rate of fibrillation d...
The work introduces a localized surface plasmon resonance (LSPR) sensor chip integrated with vertical-cavity surface-emitting lasers (VCSELs). Using VCSEL as the light source, the hexagonal gold nanoparticle array was integrated with anodic aluminum...
Terahertz (THz) metamaterial biosensors have emerged as a powerful platform for label-free, non-ionizing biodetection, yet their clinical translation is severely hindered by limited sensitivity, poor anti-interference capability, and a fragmented res...
Molecular dynamics techniques provide numerous strategies for investigating biomolecular energetics, though quantitative analysis is often only accessible for relatively small (frequently monomeric) systems. To address this limit, we use simulations...
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