Performance of reservoir discretizations in quantum transport simulations.

Quantum transport simulations often use explicit, yet finite, electronic reservoirs. These should converge to the correct continuum limit, albeit with a trade-off between discretization and computational cost. Here, we study this interplay for extended reservoir simulations, where relaxation maintains a bias or temperature drop across the system.

Open System Tensor Networks and Kramers' Crossover for Quantum Transport.

Tensor networks are a powerful tool for many-body ground states with limited entanglement. These methods can nonetheless fail for certain time-dependent processes-such as quantum transport or quenches-where entanglement growth is linear in time. Matrix-product-state decompositions of the resulting out-of-equilibrium states require a bond dimension that grows exponentially, imposing a hard limit on simulation timescales.

Topology, landscapes, and biomolecular energy transport.

While ubiquitous, energy redistribution remains a poorly understood facet of the nonequilibrium thermodynamics of biomolecules. At the molecular level, finite-size effects, pronounced nonlinearities, and ballistic processes produce behavior that diverges from the macroscale. Here, we show that transient thermal transport reflects macromolecular energy landscape architecture through the topological characteristics of molecular contacts and the nonlinear processes that mediate dynamics.

Optimal transport and colossal ionic mechano-conductance in graphene crown ethers.

Biological ion channels balance electrostatic and dehydration effects to yield large ion selectivity alongside high transport rates. These macromolecular systems are often interrogated through point mutations of their pore domain, limiting the scope of mechanistic studies. In contrast, we demonstrate that graphene crown ether pores afford a simple platform to directly investigate optimal ion transport conditions, i.

A spin-1 representation for dual-funnel energy landscapes.

The interconversion between the left- and right-handed helical folds of a polypeptide defines a dual-funneled free energy landscape. In this context, the funnel minima are connected through a continuum of unfolded conformations, evocative of the classical helix-coil transition. Physical intuition and recent conjectures suggest that this landscape can be mapped by assigning a left- or right-handed helical state to each residue.

Communication: Master equations for electron transport: The limits of the Markovian limit.

Master equations are increasingly popular for the simulation of time-dependent electronic transport in nanoscale devices. Several recent Markovian approaches use "extended reservoirs"-explicit degrees of freedom associated with the electrodes-distinguishing them from many previous classes of master equations. Starting from a Lindblad equation, we develop a common foundation for these approaches.

Visible-Light-Responsive Graphitic Carbon Nitride: Rational Design and Photocatalytic Applications for Water Treatment.

Graphitic carbon nitride (g-CN) has recently emerged as a promising visible-light-responsive polymeric photocatalyst; however, a molecular-level understanding of material properties and its application for water purification were underexplored. In this study, we rationally designed nonmetal doped, supramolecule-based g-CN with improved surface area and charge separation. Density functional theory (DFT) simulations indicated that carbon-doped g-CN showed a thermodynamically stable structure, promoted charge separation, and had suitable energy levels of conduction and valence bands for photocatalytic oxidation compared to phosphorus-doped g-CN.

Computational modeling of self-trapped electrons in rutile TiO2.

In conjunction with the constrained density functional theory, a valence-bond representation has been employed to model the migration of anionic polaron in bulk rutile TiO2. It was found that the charge delocalization of a self-trapped electron proceeded predominately along the c crystal axis of rutile, thus exhibiting pronounced directional heterogeneity of polaron migration. As a result, the extrapolated polaron activation energies are 0.

Ab initio dynamics of the cytochrome P450 hydroxylation reaction.

The iron(IV)-oxo porphyrin π-cation radical known as Compound I is the primary oxidant within the cytochromes P450, allowing these enzymes to affect the substrate hydroxylation. In the course of this reaction, a hydrogen atom is abstracted from the substrate to generate hydroxyiron(IV) porphyrin and a substrate-centered radical. The hydroxy radical then rebounds from the iron to the substrate, yielding the hydroxylated product.

Spin equilibrium and O₂-binding kinetics of Mycobacterium tuberculosis CYP51 with mutations in the histidine-threonine dyad.

The acidic residues of the "acid-alcohol pair" in CYP51 enzymes are uniformly replaced with histidine. Herein, we adopt the Mycobacterium tuberculosis (mt) enzyme as a model system to investigate these residues' roles in finely tuning the heme conformation, iron spin state, and formation and decay of the oxyferrous enzyme. Properties of the mtCYP51 and the T260A, T260V, and H259A mutants were interrogated using UV-Vis and resonance Raman spectroscopies.

Solvatochromism and the solvation structure of benzophenone.

Many complex molecular phenomena, including macromolecular association, protein folding, and chemical reactivity, are determined by the nuances of their electrostatic landscapes. The measurement of such electrostatic effects is nonetheless difficult, and is typically accomplished by exploiting a spectroscopic probe within the system of interest, such as through the vibrational Stark effect. Raman spectroscopy and solvatochromism afford an alternative to this method, circumventing the limitations of infrared spectroscopy, providing a lower detection limit, and permitting measurement in a native chemical environment.

Cytochrome P450 compound I in the plane wave pseudopotential framework: GGA electronic and geometric structure of thiolate-ligated iron(IV)-oxo porphyrin.

The cytochromes P450 constitute a ubiquitous family of metalloenzymes, catalyzing manifold reactions of biological and synthetic importance via a thiolate-ligated iron-oxo (IV) porphyrin radical species denoted compound I (Cpd I). Experimental investigations have implicated this intermediate in a broad spectrum of biophysically interesting phenomena, further augmenting the importance of a Cpd I model system. Ab initio molecular dynamics, including Car-Parrinello and path integral methods, conjoin electronic structure theory with finite temperature simulation, affording tools most valuable to approach such enzymes.

A GGA+U approach to effective electronic correlations in thiolate-ligated iron-oxo (IV) porphyrin.

High-valent oxo-metal complexes exhibit correlated electronic behavior on dense, low-lying electronic state manifolds, presenting challenging systems for electronic structure methods. Among these species, the iron-oxo (IV) porphyrin denoted Compound I occupies a privileged position, serving a broad spectrum of catalytic roles. The most reactive members of this family bear a thiolate axial ligand, exhibiting high activity toward molecular oxygen activation and substrate oxidation.

Free energy landscape of the retinol/serum retinol binding protein complex: a biological host-guest system.

Small molecule host-guest complexes have traditionally provided model systems for biological ligand recognition. Nonetheless, direct extrapolation of these results is precluded by the comparative simplicity of these supramolecular assemblies. If energetic behavior analogous to small molecule host-guest chemistry exists, it is unclear how this would manifest for protein-small molecule interactions.

Interaction of the sigma(2) receptor ligand PB28 with the human nucleosome: computational and experimental probes of interaction with the H2A/H2B dimer.

Sigma-2 (sigma(2)) binding sites are an emerging target for anti-neoplastic agents due to the strong apoptotic effect exhibited by sigma(2) agonists in vitro and the overexpression of these sites in tumor cells. Nonetheless, no sigma(2) receptor protein has been identified. Affinity chromatography using the high-affinity sigma(2) ligand PB28 and human SK-N-SH neuroblastoma cells was previously utilized to identify sigma(2) ligand binding proteins, specifically histones H1, H2A, H2B, and H3.