26 papers · ranked by Valyu relevance
Biman Bagchi
Established theoretical studies of diffusion in rugged (or rough) potential surfaces have largely focused on quenched energy landscapes. Here we study diffusion on a rugged energy landscape in the presence of dynamic disorder, a situation relevant to a wide range of disordered systems, including glasses, disordered…
Piotr Polanowski, Andrzej Sikorski, Jose Luis Riccardo, Antonio J. Ramirez-Pastor
The dynamics of dense colloidal systems are not fully understood. In the study of these types of systems, computer simulations based on the so-called hard sphere model play a significant role. In the presented work, we consider a system of hard spheres of the same size but different mobilities (molecules with high…
Megan A. Steves, Ke Xu
Wide-field single-molecule tracking is often limited by the ~10 ms camera frame time. We introduce SpeedyTrack, which directly enables microsecond wide-field single-molecule tracking/imaging on common setups. Harnessing the native sub-microsecond vertical charge shifting capability of EM-CCDs, SpeedyTrack staggers…
Ralf Biehl, Margarita Kruteva, Orsolya Czakkel, Ingo Hoffmann + 2 more
A fundamental feature of the antibody structure is the flexible linker between the 3 fragments that allows great flexibility and simultaneous binding to epitopes of antigens and receptors. Combining dynamic light scattering, neutron spin-echo spectroscopy and PFG-NMR we determine characteristic internal fragment…
Vittorio Bariosco, Stefano Pantaleone, Cecilia Ceccarelli, Piero Ugliengo + 1 more
ab Initio Kinetic Monte Carlo Approach for Modeling Adsorption and Diffusion in Interstellar Icy Grain Mantles: The Case of H 2 S Authors: Vittorio Bariosco, Stefano Pantaleone, Cecilia Ceccarelli, Piero Ugliengo, Albert Rimola Understanding diffusion on interstellar ices is key to modeling the chemical evolution of…
Manuel Mayo, M. I. García de Soria, P. Maynar, J. Javier Brey
The self-diffusion process of a hard sphere fluid confined by two parallel plates separated by a distance on the order of the particle diameter is studied. The starting point is a closed kinetic equation for the distribution function that takes into account the effects of the confinement and that is valid in the…
Harsa Mitra, Prasheel Nakate, Madeline Stevenson, Arezoo M. Ardekani
Efficient drug delivery using nanoparticles (NPs) critically depends on their ability to diffuse through biological tissues to reach target cells at therapeutic concentrations. The extracellular matrix (ECM) poses a key barrier to such transport, which directly influences bio-distribution, cellular uptake, and overall…
Authors not listed
Direct air capture (DAC) using amine-functionalised adsorbents is a promising route to negative emissions. Here, we investigate how humidity influences the swelling, CO2 uptake, and mass transfer of two amine-functionalised polymeric resins, Lewatit VP OC 1065 and Purolite A110, using a combined experimental and…
C. Reichhardt, C. J. O. Reichhardt
Self-propelled active matter can exhibit vastly different behavior than systems with purely Brownian motion. In Eur. Phys. J. E 40, 23 (2017), Zeitz, Wolf, and Stark compared an active matter particle with a Brownian particle moving in a random obstacle array. They showed that near the obstacle percolation density…
Evangelia Nathanail, Edoardo Rolando, Max Ruwolt, Iryna Zaporozhets + 3 more
Mitochondrial crista junctions (CJs) operate as regulated gateways into the cristae microenvironment, whose protein, metabolite, and ion compositions are finely tuned for mitochondrial function. The Mic60-Mic19 complex of the mitochondrial contact site and cristae organizing system (MICOS) complex was suggested to span…
de Tournemire, Guirec, Fares, Nicolas + 4 more
The encounter of diffusing entities underlies a wide range of natural phenomena. The dynamics of these first-passage processes are strongly influenced by the geometry of the system, for example through confining boundaries. Confinement, which alters the diffusion of microscopic particles through both conservative and…
Xinyue Cui, Lingyu Ge, Xinguang Yang, Xuhui Li + 3 more
Protein conformational ensembles encode the dynamic landscapes underlying biological function, regulation, and allostery. Accurately reconstructing such ensembles while balancing conformational distributions accuracy and physical plausibility remains a fundamental challenge in structural biology, particularly when…
Andrei Pantea, Luca Biferale, Michele Buzzicotti, Guillaume Charpiat + 2 more
Recent advances in data-driven modeling have shown that diffusion models can successfully generate synthetic Lagrangian trajectories in turbulent flows. Building on this progress, we extend the method to the joint generation of pairs of Lagrangian velocity trajectories, enabling a fully data-driven representation of…
Bin Sun, Alec Loftus, Peter Kekenes-Huskey
We review the Brownian dynamics (BD) modeling of biomolecular binding events, with an emphasis on enzyme-substrate interactions in cellular environments. We begin with theoretical foundations of BD and its applications to association and dissociation binding processes in both homogeneous and heterogeneous media. Next…
Aiyan Brown, Claudiu C. Gradinaru
Single-molecule Förster Resonance Energy Transfer (smFRET) affords access to nanometre-scale structural and kinetic information for individual biomolecular species. Conventional analyses presuppose a strict separation of the underlying dynamical processes into distinct timescales - an assumption that is frequently…
Eden Chang, Zhejing Xu, Elliott W. Z. Weix, Scott M. Coyle
Cells self-organize complex internal architectures through an interplay between biochemical signaling and physical structure. Within this paradigm, reaction-diffusion signaling mechanisms create local concentration gradients, and protein condensates assemble in a concentration-dependent manner, providing a natural…
Vivek Sharma, Kolade Adebowale, Ze Gong, Ovijit Chaudhuri + 1 more
Cell migration is pivotal in cancer metastasis, where cells navigate the extracellular matrix (ECM) and invade distant tissues. While the ECM is viscoelastic, exhibiting time-dependent stress relaxation, its influence on cell migration remains poorly understood. Here, we employ an integrated experimental and modeling…
Authors not listed
The persistent pharmaceutical pollutant carbamazepine (CBZ) poses a significant challenge to conventional wastewater treatment, with hydrophobic zeolites emerging as promising selective adsorbents. However, the possibility of diffusion within these tightly confining pores remains poorly understood and computational…
Authors not listed
Atomistic simulations provide essential mechanistic insights into chemical processes, yet many important phenomena in chemistry and materials science occur on timescales that are inaccessible to molecular dynamics. Existing computational approaches force a choice between atomic resolution on relatively short timescales…
Denis S. Grebenkov
Autocatalytic processes underlie diverse systems in which replication is triggered at interfaces, including heterogeneous catalysis on solid substrates, enzyme activity at membranes, viral infections, biofilm growth, and spatially structured ecosystems. In a typical scenario, particles move in a bulk medium and…
Authors not listed
Picosecond electric field fluctuations mediate local environments that govern electrocatalysis at the electrode-water interface. Consequently, cosolvents modulate hydrogen-bond networks and interfacial dynamics. Here, we use surface-enhanced two-dimensional infrared (SE 2D IR) spectroscopy to quantify the effect of the…
Authors not listed
Predicting how often molecules collide in dilute solution remains a long-standing challenge often with several orders of magnitude difference between theoretical values and experimental values also among different experimental values. Traditional frameworks from Smoluchowski and Langmuir rely on the formation of stable…
János Végh
Ions in electrolytes can have coatings and can combine into different complexes that significantly affects their size, mass, and transport features. Measuring such coatings of ions traveling in narrow, limited spaces inside biological objects is challenging. We assumed that the coating changes the size of the ion and…
Elad Noor, Kirill Jefimov, Ersilia Bifulco, Evgeny Onischenko
Cells continuously produce and degrade multiple small and large molecules, essential for maintaining homeostasis. The study of these dynamics has gained momentum since the development of pulse-chase and wash-in/out methods, utilizing fluorescent or isotopic labeling of cellular components to assess properties such as…
Authors not listed
Molecular dynamics (MD) and hybrid quantum–classical (QM/MM) methods provide powerful tools for simulating chemical and biological systems, yet their application to long-timescale, strongly coupled processes remains limited by non-integrability, chaotic sensitivity, and extreme time-scale separation. These limitations…
Authors not listed
Hyperpolarization of biological samples by dynamic dissolution nuclear polarization (dDNP) has opened new perspectives for the time resolved observation of fast chemical processes by NMR, offering unprecedented sensitivity and temporal resolution. Among these processes, anomerization (the interconversion between the α…