Preface: Special Topic on Coarse Graining of Macromolecules, Biopolymers, and Membranes.

This special issue highlights new developments in theory and coarse-graining in biological and synthetic macromolecules and membranes. Such approaches give unique insights into the principles and design of the structures, dynamics, and assembly processes of these complex fluids and soft materials, where the length and time scales are often prohibitively long for fully atomistic modeling.

Modeling microcirculatory blood flow: current state and future perspectives.

Microvascular blood flow determines a number of important physiological processes of an organism in health and disease. Therefore, a detailed understanding of microvascular blood flow would significantly advance biophysical and biomedical research and its applications. Current developments in modeling of microcirculatory blood flow already allow to go beyond available experimental measurements and have a large potential to elucidate blood flow behavior in normal and diseased microvascular networks.

Tuning the van der Waals Interaction of Graphene with Molecules via Doping.

We use scanning tunneling microscopy to visualize and thermal desorption spectroscopy to quantitatively measure that the binding of naphthalene molecules to graphene, a case of pure van der Waals interaction, strengthens with n and weakens with p doping of graphene. Density-functional theory calculations that include the van der Waals interaction in a seamless, ab initio way accurately reproduce the observed trend in binding energies. Based on a model calculation, we propose that the van der Waals interaction is modified by changing the spatial extent of graphene's π orbitals via doping.

Hydrodynamic correlations in shear flow: Multiparticle-collision-dynamics simulation study.

The nonequilibrium hydrodynamic correlations of a multiparticle-collision-dynamics (MPC) fluid in shear flow are studied by analytical calculations and simulations. The Navier-Stokes equations for a MPC fluid are linearized about the shear flow and the hydrodynamic modes are evaluated as an expansion in the wave vector. The shear-rate dependence and anisotropy of the transverse and longitudinal velocity correlations are analyzed.

Modulated escape from a metastable state driven by colored noise.

Many phenomena in nature are described by excitable systems driven by colored noise. The temporal correlations in the fluctuations hinder an analytical treatment. We here present a general method of reduction to a white-noise system, capturing the color of the noise by effective and time-dependent boundary conditions.

Physics of active jamming during collective cellular motion in a monolayer.

Although collective cell motion plays an important role, for example during wound healing, embryogenesis, or cancer progression, the fundamental rules governing this motion are still not well understood, in particular at high cell density. We study here the motion of human bronchial epithelial cells within a monolayer, over long times. We observe that, as the monolayer ages, the cells slow down monotonously, while the velocity correlation length first increases as the cells slow down but eventually decreases at the slowest motions.

Controlling the Electronic Structures and Properties of in-Plane Transition-Metal Dichalcogenides Quantum Wells.

In-plane transition-metal dichalcogenides (TMDs) quantum wells have been studied on the basis of first-principles density functional calculations to reveal how to control the electronic structures and the properties. In collection of quantum confinement, strain and intrinsic electric field, TMD quantum wells offer a diverse of exciting new physics. The band gap can be continuously reduced ascribed to the potential drop over the embedded TMD and the strain substantially affects the band gap nature.

Dynamic effective connectivity in cortically embedded systems of recurrently coupled synfire chains.

As a candidate mechanism of neural representation, large numbers of synfire chains can efficiently be embedded in a balanced recurrent cortical network model. Here we study a model in which multiple synfire chains of variable strength are randomly coupled together to form a recurrent system. The system can be implemented both as a large-scale network of integrate-and-fire neurons and as a reduced model.

Perpendicular reading of single confined magnetic skyrmions.

Thin-film sub-5 nm magnetic skyrmions constitute an ultimate scaling alternative for future digital data storage. Skyrmions are robust noncollinear spin textures that can be moved and manipulated by small electrical currents. Here we show here a technique to detect isolated nanoskyrmions with a current perpendicular-to-plane geometry, which has immediate implications for device concepts.

Cation Selectivity in Biological Cation Channels Using Experimental Structural Information and Statistical Mechanical Simulation.

Cation selective channels constitute the gate for ion currents through the cell membrane. Here we present an improved statistical mechanical model based on atomistic structural information, cation hydration state and without tuned parameters that reproduces the selectivity of biological Na+ and Ca2+ ion channels. The importance of the inclusion of step-wise cation hydration in these results confirms the essential role partial dehydration plays in the bacterial Na+ channels.

Oxygen orders differently under graphene: new superstructures on Ir(111).

Using scanning tunneling microscopy, the oxygen adsorbate superstructures on bare Ir(111) are identified and compared to the ones formed by intercalation in between graphene and the Ir(111) substrate. For bare Ir(111) we observe O-(2 × 2) and O-(2 × 1) structures, thereby clarifying a persistent uncertainty about the existence of these structures and the role of defects for their stability. For the case of graphene-covered Ir(111), oxygen intercalation superstructures can be imaged through the graphene monolayer by choosing proper tunneling conditions.

New type of stable particlelike states in chiral magnets.

We present a new type of thermodynamically stable magnetic state at interfaces and surfaces of chiral magnets. The state is a soliton solution of micromagnetic equations localized in all three dimensions near a boundary, and it contains a singularity but nevertheless has finite energy. Both features combine to form a quasiparticle state for which we expect unusual transport and dynamical properties.

Understanding particle margination in blood flow - A step toward optimized drug delivery systems.

Targeted delivery of drugs and imaging agents is very promising to develop new strategies for the treatment of various diseases such as cancer. For an efficient targeted adhesion, the particles have to migrate toward the walls in blood flow - a process referred to as margination. Due to a huge diversity of available carriers, a good understanding of their margination properties in blood flow depending on various flow conditions and particle properties is required.

Scalability of Asynchronous Networks Is Limited by One-to-One Mapping between Effective Connectivity and Correlations.

Network models are routinely downscaled compared to nature in terms of numbers of nodes or edges because of a lack of computational resources, often without explicit mention of the limitations this entails. While reliable methods have long existed to adjust parameters such that the first-order statistics of network dynamics are conserved, here we show that limitations already arise if also second-order statistics are to be maintained. The temporal structure of pairwise averaged correlations in the activity of recurrent networks is determined by the effective population-level connectivity.

Conformations, hydrodynamic interactions, and instabilities of sedimenting semiflexible filaments.

The conformations and dynamics of semiflexible filaments subject to a homogeneous external (gravitational) field, e.g., in a centrifuge, are studied numerically and analytically.

Self-propelled worm-like filaments: spontaneous spiral formation, structure, and dynamics.

Worm-like filaments that are propelled homogeneously along their tangent vector are studied by Brownian dynamics simulations. Systems in two dimensions are investigated, corresponding to filaments adsorbed to interfaces or surfaces. A large parameter space covering weak and strong propulsion, as well as flexible and stiff filaments is explored.

Orbitals from local RDMFT: Are they Kohn-Sham or natural orbitals?

Recently, an approximate theoretical framework was introduced, called local reduced density matrix functional theory (local-RDMFT), where functionals of the one-body reduced density matrix (1-RDM) are minimized under the additional condition that the optimal orbitals satisfy a single electron Schrödinger equation with a local potential. In the present work, we focus on the character of these optimal orbitals. In particular, we compare orbitals obtained by local-RDMFT with those obtained with the full minimization (without the extra condition) by contrasting them against the exact NOs and orbitals from a density functional calculation using the local density approximation (LDA).

Two-Dimensional Topological Crystalline Insulator and Topological Phase Transition in TlSe and TlS Monolayers.

The properties that distinguish topological crystalline insulator (TCI) and topological insulator (TI) rely on crystalline symmetry and time-reversal symmetry, respectively, which encodes different bulk and surface/edge properties. Here, we predict theoretically that electron-doped TlM (M = S and Se) (110) monolayers realize a family of two-dimensional (2D) TCIs characterized by mirror Chern number CM = -2. Remarkably, under uniaxial strain (≈ 1%), a topological phase transition between 2D TCI and 2D TI is revealed with the calculated spin Chern number CS = -1 for the 2D TI.

Dzyaloshinskii-Moriya Interaction and Hall Effects in the Skyrmion Phase of Mn(1-x) Fe(x)Ge.

We carry out density functional theory calculations which demonstrate that the electron dynamics in the Skyrmion phase of Fe-rich Mn_{1-x}Fe_{x}Ge alloys is governed by Berry phase physics. We observe that the magnitude of the Dzyaloshinskii-Moriya interaction directly related to the mixed space-momentum Berry phases, changes sign and magnitude with concentration x in direct correlation with the data of Shibata et al. [Nat.

Effect of fluid-colloid interactions on the mobility of a thermophoretic microswimmer in non-ideal fluids.

Janus colloids propelled by light, e.g., thermophoretic particles, offer promising prospects as artificial microswimmers.

Substrate Specificity, Inhibitor Selectivity and Structure-Function Relationships of Aldo-Keto Reductase 1B15: A Novel Human Retinaldehyde Reductase.

Human aldo-keto reductase 1B15 (AKR1B15) is a newly discovered enzyme which shares 92% amino acid sequence identity with AKR1B10. While AKR1B10 is a well characterized enzyme with high retinaldehyde reductase activity, involved in the development of several cancer types, the enzymatic activity and physiological role of AKR1B15 are still poorly known. Here, the purified recombinant enzyme has been subjected to substrate specificity characterization, kinetic analysis and inhibitor screening, combined with structural modeling.

Attenuated Neural Processing of Risk in Young Adults at Risk for Stimulant Dependence.

Objective: Approximately 10% of young adults report non-medical use of stimulants (cocaine, amphetamine, methylphenidate), which puts them at risk for the development of dependence. This fMRI study investigates whether subjects at early stages of stimulant use show altered decision making processing.

Methods: 158 occasional stimulants users (OSU) and 50 comparison subjects (CS) performed a "risky gains" decision making task during which they could select safe options (cash in 20 cents) or gamble them for double or nothing in two consecutive gambles (win or lose 40 or 80 cents, "risky decisions").

Farey sequence in the appearance of subharmonic Shapiro steps.

The largest Lyapunov exponent has been examined in the dynamical-mode locking phenomena of the ac+dc driven dissipative Frenkel-Kontorova model with deformable substrate potential. Due to deformation, large fractional and higher order subharmonic steps appear in the response function of the system. Computation of the largest Lyapunov exponent as a way to verify their presence led to the observation of the Farey sequence.

Giant adsorption of microswimmers: Duality of shape asymmetry and wall curvature.

The effect of shape asymmetry of microswimmers on their adsorption capacity at confining channel walls is studied by a simple dumbbell model. For a shape polarity of a forward-swimming cone, like the stroke-averaged shape of a sperm, extremely long wall retention times are found, caused by a nonvanishing component of the propulsion force pointing steadily into the wall, which grows exponentially with the self-propulsion velocity and the shape asymmetry. A direct duality relation between shape asymmetry and wall curvature is proposed and verified.