How dynamic surface restructuring impacts intra-particle catalytic cooperativity.

Recent experiments indicated that nanoparticles (NPs) might efficiently catalyze multiple chemical reactions, frequently exhibiting new phenomena. One of those surprising observations is intra-particle catalytic cooperativity, when the reactions at one active site can stimulate the reactions at spatially distant sites. Theoretical explanations of these phenomena have been presented, pointing out the important role of charged hole dynamics.

Stochastic dynamics of hairballs in single-polymer growth.

Real-time monitoring of the single-chain growth of synthetic polymers shows that their end-to-end extension during polymerization in living conditions does not increase continuously. Instead, it remains in a non-equilibrium state, exhibiting stochastic wait-and-jump events when one end of the polymer is subjected to a constant force and the other end is clamped. This wait-and-jump observation was attributed to the stochastic formation and unwinding of conformational entanglements, referred to as hairballs, which result from intrachain and non-bonded interactions within the polymer.

Macromolecular Crowding Facilitates ssDNA Capture within Biological Nanopores: Role of Size Variation and Solution Heterogeneity.

Genetic sequencing is a vital process that requires the transport of charged nucleic acids through transmembrane nanopores. Single-molecule studies show that macromolecular bulk crowding facilitates the capture of these polymers, leading to a high throughput of nanopore sensors. Motivated by these observations, a minimal discrete-state stochastic framework was developed to describe the role of poly(ethylene glycol) (PEG) crowders in varying concentrations in the transport of ssDNA through α-hemolysin nanopores.

How Heterogeneity Affects Cooperative Communications within Single Nanocatalysts.

Catalysis remains one of the most essential methods in chemical research and industry. Recent experiments have discovered an unusual phenomenon of catalytic cooperativity, when a reaction at one active site can stimulate reactions at neighboring sites within single nanoparticles. While theoretical analysis established that the transport of charged holes is responsible for this phenomenon, it does not account for inhomogeneity in the structural and dynamic properties of single nanocatalysts.

Microscopic Mechanism of Macromolecular Crowder-Assisted DNA Capture and Translocation through Biological Nanopores.

Biological nanopore sensors are widely used for genetic sequencing as nucleic acids and other molecules translocate through them across membranes. Recent studies have shown that the transport of these polymers through nanopores is strongly influenced by macromolecular bulk crowders. By using poly(ethylene glycol) (PEG) molecules as crowders, experiments have shown an increase in the capture rates and translocation times of polymers through an α-hemolysin (αHL) nanopore, which provides high-throughput signals and accurate sensing.

Theoretical Tools to Quantify Stochastic Fluctuations in Single-Molecule Catalysis by Enzymes and Nanoparticles.

Single-molecule microscopic techniques allow the counting of successive turnover events and the study of the time-dependent fluctuations of the catalytic activities of individual enzymes and different sites on a single heterogeneous nanocatalyst. It is important to establish theoretical methods to obtain the statistical measurements of such stochastic fluctuations that provide insight into the catalytic mechanism. In this review, we discuss a few theoretical frameworks for evaluating the first passage time distribution functions using a self-consistent pathway approach and chemical master equations, to establish a connection with experimental observables.

Theoretical insights into the full description of DNA target search by subdiffusing proteins.

DNA binding proteins (DBPs) diffuse in the cytoplasm to recognise and bind with their respective target sites on the DNA to initiate several biologically important processes. The first passage time distributions (FPTDs) of DBPs are useful in quantifying the timescales of the most-probable search paths in addition to the mean value of the distribution which, strikingly, are decades of order apart in time. However, extremely crowded conditions or the viscoelasticity of the cellular medium among other factors causes biomolecules to exhibit anomalous diffusion which is usually overlooked in most theoretical studies.

Influence of Nonspecific Interactions between Proteins and Cytoplasmic Crowders in Facilitated Diffusion of Proteins: Theoretical Insights.

The binding of proteins to their respective specific sites on the DNA through facilitated diffusion serves as the initial step of various important biological processes. While this search process has been thoroughly investigated studies, the cellular environment is complex and may interfere with the protein's search dynamics. The cytosol is heavily crowded, which can potentially modify the search by nonspecifically interacting with the protein that has been mostly overlooked.

Understanding the Reaction Dynamics on Heterogeneous Catalysts Using a Simple Stochastic Approach.

Recent experimental advances on investigating nanoparticle catalysts with multiple active sites provided a large amount of quantitative information on catalytic processes. These observations stimulated significant theoretical efforts, but the underlying molecular mechanisms are still not well-understood. We introduce a simple theoretical method to analyze the reaction dynamics on catalysts with multiple active sites based on a discrete-state stochastic description and obtain a comprehensive description of the dynamics of chemical reactions on such catalysts.