Related papers: Single-molecule experiments in biological physics:…
Human physiology and pathology arise from the coordinated interactions of diverse single cells. However, analyzing single cells has been limited by the low sensitivity and throughput of analytical methods. DNA sequencing has recently made…
The Chemical Master Equation (CME) provides a highly accurate, yet extremely resource-intensive representation of a stochastic chemical reaction network and its kinetics due to the exponential scaling of its possible states with the number…
Decades of hardware, methodological, and algorithmic development have propelled molecular dynamics (MD) simulations to the forefront of materials-modeling techniques, bridging the gap between electronic-structure theory and continuum…
Single-cell technologies have revolutionized biomedical research by enabling scalable measurement of the genome, transcriptome, and proteome of multiple systems at single-cell resolution. Now widely applied to cancer models, these assays…
Scanning tunneling microscope (STM) has presented a revolutionary methodology to the nanoscience and nanotechnology. It enables imaging the topography of surfaces, mapping the distribution of electronic density of states, and manipulating…
We present a theory for analyzing residence times of single molecules in a fixed detection area of a scanning tunneling microscope (STM). The approach is developed for one-dimensional molecule diffusion and can be extended to two dimensions…
We discuss implications of a recent experimental breakthrough which uses a fluorescence-doped flexible semiconducting polymer to construct a single-molecule sensor which can detect ultra-weak forces in the molecular environment, with a grey…
Many pressing medical challenges - such as diagnosing disease, enhancing directed stem cell differentiation, and classifying cancers - have long been hindered by limitations in our ability to quantify proteins in single cells.…
The study of biomolecular folding has been greatly advanced by single-molecule force spectroscopy (SMFS), which enables the observation of the dynamics of individual molecules. However, extracting quantitative models of fundamental…
Single-cell proteomics (SCP) is transforming our understanding of biological complexity by shifting from bulk proteomics, where signals are averaged over thousands of cells, to the proteome analysis of individual cells. This granular…
Analyzing proteins from single cells by tandem mass spectrometry (MS) has become technically feasible. While such analysis has the potential to accurately quantify thousands of proteins across thousands of single cells, the accuracy and…
The solvation free energy (SFE) of molecules and ions is a fundamental property governing their solvation behavior and solubility. Molecular simulations offer a route to compute SFEs using alchemical free energy methods, such as…
Existing machine learning methods for molecular (e.g., gene) embeddings are restricted to specific tasks or data modalities, limiting their effectiveness within narrow domains. As a result, they fail to capture the full breadth of gene…
With the rapid advancement of computational techniques, Molecular Dynamics (MD) simulations have emerged as powerful tools in biomedical research, enabling in-depth investigations of biological systems at the atomic level. Among the diverse…
Modeling and simulation (M&S) has revolutionized the way modern engineered products are designed, tested and evaluated. Yet modeling and simulation is much less frequently applied in the study of natural biological and active matter…
The smooth particle mesh Ewald (SPME) method is the standard method for computing the electrostatic interactions in the molecular simulations. In this work, the multiple staggered mesh Ewald (MSME) method is proposed to boost the accuracy…
Achieving dynamic manipulation and control of single molecules at high spatio-temporal resolution is pivotal for advancing atomic-scale computing and nanorobotics. However, this endeavour is critically challenged by complex nature of atomic…
Stochastic models of reaction-diffusion systems are important for the study of biochemical reaction networks where species are present in low copy numbers or if reactions are highly diffusion limited. In living cells many such systems…
We explore theoretically the electroluminescence of single molecules. We adopt a local-electrode framework that is appropriate for scanning tunneling microscopy (STM) experiments where electroluminescence originates from individual…
Emergent phenomena share the fascinating property of not being obvious consequences of the design of the system in which they appear. This characteristic is no less relevant when attempting to simulate such phenomena, given that the outcome…