**2020**

**Adiabatic motion and statistical mechanics***via*mass-zero constrained dynamics

Sara Bonella, Alessandro Coretti, Rodolphe Vuilleumier and Giovanni Ciccotti, Physical Chemistry Chemical Physics (2020)

DOI: 10.1039/D0CP00163E**Abstract:**In recent work [Coretti*et al.*,*J. Chem. Phys.*, 2018,**149**, 191102], a new algorithm to solve numerically the dynamics of the shell model for polarization was presented. The approach, broadly applicable to systems involving adiabatically separated dynamical variables, employs constrained molecular dynamics to strictly enforce the condition that the force on the fast degrees of freedom, modeled as having zero mass, is null at each time step. The algorithm is symplectic and fully time reversible, and results in stable and efficient propagation. In this paper we complete the discussion of the mechanics of mass-zero constrained dynamics by showing how to adapt it to problems where the fast degrees of freedom must satisfy additional conditions. This extension includes, in particular, the important case of first principles molecular dynamics. We then consider the statistical mechanics of the mass-zero constrained dynamical system demonstrating that the marginal probability sampled by the dynamics in the physical phase space recovers the form of the Born–Oppenheimer probability density. The effectiveness of the approach and the favorable scaling of the algorithm with system size are illustrated in test calculations of solid Na*via*orbital-free density functional dynamics.

**Towards extreme scale dissipative particle dynamics simulations using multiple GPGPUs**

J. Castagna, X. Guo, M. Seaton and A. O’Cais, Computer Physics Communications (2020) 107159

DOI: 10.1016/j.cpc.2020.107159 (open access)**Abstract:**A multi-GPGPU development for Mesoscale Simulations using the Dissipative Particle Dynamics method is presented. This distributed GPU acceleration development is an extension of the DL_MESO package to MPI+CUDA in order to exploit the computational power of the latest NVIDIA cards on hybrid CPU–GPU architectures. Details about the extensively applicable algorithm implementation and memory coalescing data structures are presented. The key algorithms’ optimizations for the nearest-neighbour list searching of particle pairs for short range forces, exchange of data and overlapping between computation and communications are also given. We have carried out strong and weak scaling performance analyses with up to 4096 GPUs. A two phase mixture separation test case with 1.8 billion particles has been run on the Piz Daint supercomputer from the Swiss National Supercomputer Center. With CUDA aware MPI, proper GPU affinity, communication and computation overlap optimizations for multi-GPU version, the final optimization results demonstrated more than 94% efficiency for weak scaling and more than 80% efficiency for strong scaling. As far as we know, this is the first report in the literature of DPD simulations being run on this large number of GPUs. The remaining challenges and future work are also discussed at the end of the paper.

**2019**

**Atomistic insight into the kinetic pathways for Watson-Crick to Hoogsteen transitions in DNA**

Vreede J, Pérez de Alba Ortíz A, Bolhuis PG, and Swenson DWH,*Nucleic Acids Research***2019**, Vol. 47, No. 21, 11069–11076

DOI: 10.1093/nar/gkz837 (open access)**Synopsis:**DNA predominantly contains Watson–Crick (WC) base pairs, but a non-negligible fraction of base pairs are in the Hoogsteen (HG) hydrogen bonding motif at any time. In the HG motif, the purine is “upside down” compared to the WC motif. Two classes of mechanism have been proposed for the transition between these motifs: one where the base pair stays inside the confines of the helical backbone, and one where one base flips outside of the helical backbone before returning in the “upside down” HG conformation. The transitions between WC and HG may play a role in recognition and replication, but are difficult to investigate because they occur quickly, but only rarely. To gain insight into the mechanisms for this process, researchers performed transition path sampling simulations on a model nucleotide sequence in which an adenine-thymine base pair changes from WC to HG, and found that the outside transition was strongly preferred. Simulated rates and free energy differences agree with experiments, the simulations provide highly detailed insights into the mechanisms of this process.

**Local control theory for supercomputing qubits**

M. Mališ, P. KI. Barkoutsos, M. Ganzhorn, S. Filipp, D. J. Egger, S. Bonella and I. Tavernelli,*Phys. Rev. A***99**, 052316

DOI: 10.1103/PhysRevA.99.052316 (open access)**Synopsis:**In this work, we develop a method to design control pulses for fixed-frequency superconducting qubits coupled via tunable couplers based on local control theory, an approach commonly employed to steer chemical reactions. Local control theory provides an algorithm for the monotonic population transfer from a selected initial state to a desired final state of a quantum system through the on-the-fly shaping of an external pulse. The method, which only requires a unique forward time-propagation of the system wavefunction, can serve as starting point for additional refinements that lead to new pulses with improved properties. Among others, we propose an algorithm for the design of pulses that can transfer population in a reversible manner between given initial and final states of coupled fixed-frequency superconducting qubits.

**The Fluctuation−Dissipation Theorem as a Diagnosis and Cure for Zero-Point Energy Leakage in Quantum Thermal Bath Simulations**

Etienne Mangaud, Simon Huppert, Thomas Plé, Philippe Depondt, Sara Bonella, Fabio Finocchi,*J. Chem. Theory Comput.***2019**, 15, 2863-2880

DOI: 10.1021/acs.jctc.8b01164**Synopsis:**Quantum thermal bath (QTB) simulations reproduce statistical nuclear quantum effects via a Langevin equation with a coloured random force. Although this approach has proven efficient for a variety of chemical and condensed-matter problems, the QTB, as many other semiclassical methods, suffers from zero-point energy leakage (ZPEL). The absence of a reliable criterion to quantify the ZPEL without resorting to demanding comparisons with path integral based calculations has so far hindered the use of the QTB for the simulation of real systems. In this work, we establish a quantitative connection between ZPEL in the QTB framework and deviations from the quantum fluctuation-dissipation theorem (FDT) that can be monitored along the simulation. This provides a rigorous general criterion to detect and quantify the ZPEL without any*a priori*knowledge of the system under study.

**ESPResSo++ 2.0: Advanced methods for multiscale molecular simulation**

Horacio V. Guzman, Nikita Tretyakov, Hideki Kobayashi, Aoife C. Fogarty, Karsten Kreis, Jakub Krajniak, Christoph Junghans, Kurt Kremer, Torsten Stuehn,*Computer Physics Communications***2019**, 238, 66–76

DOI: 10.1016/j.cpc.2018.12.017

Open access version

**Abstract:**Molecular simulation is a scientific tool used in many fields including material science and biology. This requires constant development and enhancement of algorithms within molecular simulation software packages. Here, we present computational tools for multiscale modeling developed and implemented within the ESPResSo++ package. These include the latest applications of the adaptive resolution scheme, the hydrodynamic interactions through a lattice Boltzmann solvent coupled to particle-based molecular dynamics, the implementation of the hierarchical strategy for equilibrating long-chained polymer melts and a heterogeneous spatial domain decomposition. The software design of ESPResSo++ has kept its highly modular C++ kernel with a Python user interface. Moreover, it has been enhanced by automatic scripts that parse configurations from other established packages, providing scientists with the ability to rapidly set up their simulations.

**Molecular Dynamics of Open Systems: Construction of a Mean‐Field Particle Reservoir**

Luigi Delle Site, Christian Krekeler, John Whittaker, Animesh Agarwal, Rupert Klein, Felix Höfling,*Adv. Theory Simul.***2019**, 1900014

DOI: 10.1002/adts.201900014 (Open access)**Synopsis**: A procedure for the construction of a particle and energy reservoir for the simulation of open molecular systems is presented. The reservoir is made of non‐interacting particles (tracers), embedded in a mean‐field. The tracer molecules acquire atomistic resolution upon entering the atomistic region, while atomistic molecules become tracers after crossing the atomistic boundary.

**OpenPathSampling: A Python Framework for Path Sampling Simulations. 1. Basics**

David W. H. Swenson, Jan-Hendrik Prinz, Frank Noe, John D. Chodera, and Peter G. Bolhuis,*J. Chem. Theory Comput.***2019**, 15, 813-836

DOI: 10.1021/acs.jctc.8b00626 (Open access)**Synopsis:**OpenPathSampling (OPS) is a software package to perform path sampling simulations and other trajectory-based approaches to study rare events. The methods implemented in OPS can be used to study many kinds of problems, including drug binding and unbinding, self-assembly processes, conformational changes in biomolecules, and chemical reactions. OPS is designed to be used as a library in standard Python scripts, allowing the user to create simulation suited to study their problem. It can be run interactively with tools such as Jupyter notebooks. This paper introduces the terminology used in OPS and shows how to use OPS to perform common path sampling simulations.

**OpenPathSampling: A Python Framework for Path Sampling Simulations. 2. Building and Customizing Path Ensembles and Sample Schemes**

David W. H. Swenson, Jan-Hendrik Prinz, Frank Noe, John D. Chodera, and Peter G. Bolhuis,*J. Chem. Theory Comput.***2019**, 15, 837-856

DOI: 10.1021/acs.jctc.8b00627 (Open access)**Synopsis:**Path sampling involves sampling many trajectories from a given “path ensemble,” which defines a set of conditions the trajectories must satisfy. As more path sampling methods have been developed, more and more types of path ensembles have been created. OpenPathSampling (OPS) introduces a new formalism to describe path ensembles, which unifies all of them under one framework. This paper describes this formalism, as well as other tools in OPS that could be useful to methods developers.

**2018**

**The asymmetric Wigner bilayer**

Moritz Antlanger, Gerhard Kahl, Martial Mazars, Ladislav Samaj, Emmanuel Trizac,*J. Chem. Phys.***2018**, 149, 244904

DOI: 10.1063/1.5053651

Open access version**Synopsis:**We present a comprehensive discussion of the so-called asymmetric Wigner bilayer system, where mobile point charges, all of the same sign, are immersed into the space left between two parallel, homogeneously charged plates (with possibly different charge densities). At vanishing temperatures, the particles are expelled from the slab interior; they necessarily stick to one of the two plates, and form there ordered sublattices. Using complementary tools (analytic and numerical) we study systematically the self-assembly of the point charges into ordered ground state configurations as the inter-layer separation and the asymmetry in the charge densities are varied. The overwhelming plethora of emerging Wigner bilayer ground states can be understood in terms of the competition of two strategies of the system: the desire to guarantee net charge neutrality on each of the plates and the effort of the particles to self-organise into commensurate sublattices.

**Lithium Adsorption on Graphene at finite-temperature**

Yusuf Shaidu, Emine Küçükbenli, Stefano de Gironcoli,*J. Phys. Chem. C***2018**, 122, 36, 20800-20808

DOI: 10.1021/acs.jpcc.8b05689

Open access version**Synopsis:**Graphene has been proposed as a possible alternative in Li-ion batteries to state-of-the-art graphitic anode but a first principle study of its Li-adsorption behaviour at finite temperature was still lacking. We thoroughly characterised Li adsorption on graphene, both at zero and finite temperatures by means of density functional theory (DFT), accounting for van der Waals (vdW) interactions, Monte Carlo and cluster expansion methods to sample the system phase space. Our calculations reveal two distinct types of orderings of Li on graphene, Li-gas (dispersed Li-ion) and Licluster phases. Even when vdW is included, the Li−graphene interaction is mainly electrostatic and phase separation to pristine graphene and bulk Li is energetically favourable. However, at finite temperatures, entropy allows the lesser-ordered Li-gas and Li-cluster states to be more favourable at sufficiently low concentrations: at temperatures below 400 K and concentrations below 1Li:6C, Li-gas and Li-cluster phases coexist whereas at higher concentrations, only clusters remain stable. At temperatures above 400 K, Li-gas phase can be stabilised with respect to Li cluster or Li bulk at higher concentrations.

**Unimolecular FRET sensors: Simple linker designs and properties**Shourjya Sanyal, David F. Coker, Donal MacKernan,*Nano Communication Networks***2018**, 18, 44–50

DOI: 10.1016/j.nancom.2018.10.003

Open access version**Synopsis:**The measurement of biomarkers and ligands are increasingly used to study transport, signalling, and communication in cells, and as diagnostics/prognostics of disease, or the presence of pathogens, allergens and pollutants in foods, and the environment. Accurate measurement in assays or cellular environments is important, and protein-based biosensors can be used in this context. Using simple Coarse-Grained (CG) models of unimolecular fusion protein based FRET sensors of target ligands, the authors address important questions in this paper including: Can simple CG models reproduce qualitatively experimental results? Is there an advantage in replacing flexible protein linkers with hinge-like peptides? The answers to these and other questions are disclosed in the paper.

**Adaptive resolution molecular dynamics technique: Down to the essential**

Christian Krekeler, Animesh Agarwal, Christoph Junghans, Matej Praprotnik, and Luigi Delle Site,*J. Chem. Phys.***2018**, 149, 024104

DOI: 10.1063/1.5031206

Open access version**Synopsis:**In this paper the authors study the application of the thermodynamic force in the coupling region of an adaptive resolution molecular dynamics simulation (AdResS) approach which assures thermodynamic equilibrium and proper exchange of molecules between atomistically resolved and coarse-grained regions.

**Ionic Liquids Treated within the Grand Canonical Adaptive Resolution Molecular Dynamics Technique**

B. Shadrack Jabes, Christian Krekeler,*Computation***2018**, 1, 23; doi:10.3390/computation6010023

DOI: 10.3390/computation6010023

Open access version

**Probing spatial locality in ionic liquids with the grand canonical adaptive resolution molecular dynamics technique**

B. Shadrack Jabes, C. Krekeler, R. Klein, and L. Delle Site,*J. Chem. Phys.***148**, 193804 (2018)

DOI: 10.1063/1.5009066

Open access version

**Force Field Parametrization of Metal Ions from Statistical Learning Techniques**

Francesco Fracchia, Gianluca Del Frate, Giordano Mancini, Walter Rocchia, and Vincenzo Barone,*J. Chem. Theory Comput.***2018**, 14, 255−273

DOI: 10.1021/acs.jctc.7b00779

Open access version

**2017**

**The opposing effects of isotropic and anisotropic attraction on association kinetics of proteins and colloids**

Arthur C. Newton, Ramses Kools, David W. H. Swenson, and Peter G. Bolhuis,*J. Chem. Phys.***147**, 155101(2017)

DOI: 10.1063/1.5006485

Open access version

**ζ-Glycine: insight into the mechanism of a polymorphic phase transition**

Craig L. Bull, Giles Flowitt-Hill, Stefano de Gironcoli, Emine Küçükbenli, Simon Parsons, Cong Huy Pham, Helen Y. Playforda and Matthew G. Tucker

IUCrJ, (2017). 4, 569–574

DOI: 10.1107/S205225251701096X

Open access version

**A parallel orbital-updating based plane-wave basis method for electronic structure calculations**

Yan Pana, Xiaoying Dai, Stefano de Gironcolib, Xin-Gao Gongc, Gian-Marco Rignanesed and Aihui Zhoua,*J. Comput. Phys.***2017**, 348, 482-492

DOI: 10.1016/j.jcp.2017.07.033

Open access version

**Benchmarking a Fast Proton Titration Scheme in Implicit Solvent for Biomolecular Simulations**

Fernando Luís Barroso da Silva and Donal MacKernan,*J. Chem. Theory Comput.***2017**, 13, 2915-2929

DOI: 10.1021/acs.jctc.6b01114

Open access version

**Towards Open Boundary Molecular Dynamics Simulation of Ionic Liquids**

Christian Krekeler and Luigi Delle Site,*Phys. Chem. Chem. Phys.*2017, 19, 4701-4709

DOI: 10.1039/C6CP07489H

Open access version

**Computational efficiency and Amdahl’s law for the adaptive resolution simulation technique**

Christoph Junghans, Animesh Agarwal and Luigi Delle Site,*Comput. Phys. Commun.***2017,**215, 20-25

DOI: http://dx.doi.org/10.1016/j.cpc.2017.01.030

Open access version