There is, I think, something ethereal about i —the square root of minus one. I remember first hearing about it at school. It seemed an odd beast at that time—an intruder hovering on the edge of reality.

Usually familiarity dulls this sense of the bizarre, but in the case of i it was the reverse: over the years the sense of its surreal nature intensified. It seemed that it was impossible to write mathematics that described the real world in …

I and i

The method of dispersion correction as an add-on to standard Kohn-Sham density functional theory (DFT-D) has been refined regarding higher accuracy, broader range of applicability, and less empiricism. The main new ingredients are atom-pairwise specific dispersion coefficients and cutoff radii that are both computed from first principles. The coefficients for new eighth-order dispersion terms are computed using established recursion relations. System (geometry) dependent information is used for the first time in a DFT-D type approach by employing the new concept of fractional coordination numbers (CN). They are used to interpolate between dispersion coefficients of atoms in different chemical environments. The method only requires adjustment of two global parameters for each density functional, is asymptotically exact for a gas of weakly interacting neutral atoms, and easily allows the computation of atomic forces. Three-body nonadditivity terms are considered. The method has been assessed on standard benchmark sets for inter- and intramolecular noncovalent interactions with a particular emphasis on a consistent description of light and heavy element systems. The mean absolute deviations for the S22 benchmark set of noncovalent interactions for 11 standard density functionals decrease by 15%-40% compared to the previous (already accurate) DFT-D version. Spectacular improvements are found for a tripeptide-folding model and all tested metallic systems. The rectification of the long-range behavior and the use of more accurate C(6) coefficients also lead to a much better description of large (infinite) systems as shown for graphene sheets and the adsorption of benzene on an Ag(111) surface. For graphene it is found that the inclusion of three-body terms substantially (by about 10%) weakens the interlayer binding. We propose the revised DFT-D method as a general tool for the computation of the dispersion energy in molecules and solids of any kind with DFT and related (low-cost) electronic structure methods for large systems.

http://dns2.asia.edu.tw/~ysho/YSHO-English/1000%20WC/PDF/J%20Che%20Phy132,%20154104.pdf

A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu

Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

It is shown by an extensive benchmark on molecular energy data that the mathematical form of the damping function in DFT-D methods has only a minor impact on the quality of the results. For 12 different functionals, a standard "zero-damping" formula and rational damping to finite values for small interatomic distances according to Becke and Johnson (BJ-damping) has been tested. The same (DFT-D3) scheme for the computation of the dispersion coefficients is used. The BJ-damping requires one fit parameter more for each functional (three instead of two) but has the advantage of avoiding repulsive interatomic forces at shorter distances. With BJ-damping better results for nonbonded distances and more clear effects of intramolecular dispersion in four representative molecular structures are found. For the noncovalently-bonded structures in the S22 set, both schemes lead to very similar intermolecular distances. For noncovalent interaction energies BJ-damping performs slightly better but both variants can be recommended in general. The exception to this is Hartree-Fock that can be recommended only in the BJ-variant and which is then close to the accuracy of corrected GGAs for non-covalent interactions. According to the thermodynamic benchmarks BJ-damping is more accurate especially for medium-range electron correlation problems and only small and practically insignificant double-counting effects are observed. It seems to provide a physically correct short-range behavior of correlation/dispersion even with unmodified standard functionals. In any case, the differences between the two methods are much smaller than the overall dispersion effect and often also smaller than the influence of the underlying density functional.

Effect of the damping function in dispersion corrected density functional theory

Softmode excitations in aspirin are studied with two-dimensional terahertz spectroscopy. The coupling of CH 3 rotational modes and collective excitations of π electrons results in a nonperturbative nonlinear response induced by moderate THz fields.

Strong local-field enhancement of the nonlinear softmode response in aspirin

Computational studies have shown that one or more positrons can stabilize two repelling atomic anions through the formation of two-center positronic bonds. In the present work, we study the energetic stability of a system containing two positrons and three hydride anions, namely 2e+[H33−]. To this aim, we performed a preliminary scan of the potential energy surface of the system with both electrons and positrons in a spin singlet state, with a multi-component MP2 method, that was further refined with variational and diffusion Monte Carlo calculations, and confirmed an equilibrium geometry with D3h symmetry. The local stability of 2e+[H33−] is demonstrated by analyzing the vertical detachment and adiabatic energy dissociation channels. Bonding properties of the positronic compound, such as the equilibrium interatomic distances, force constants, dissociation energies, and bonding densities are compared with those of the purely electronic H3+ and Li3+ systems. Through this analysis, we find compelling similarities between the 2e+[H33−] compound and the trilithium cation. Our results strongly point out the formation of a non-electronic three-center two-positron bond, analogous to the well-known three-center two-electron counterparts, which is fundamentally distinct from the two-center two-positron bond [D. Bressanini, J. Chem. Phys., 2021, 155, 054306], thus extending the concept of positron bonded molecules.

https://pubs.rsc.org/en/content/articlepdf/2022/sc/d2sc04630j

The three-center two-positron bond

Learning from data has led to substantial advances in a multitude of disciplines, including text and multimedia search, speech recognition, and autonomous-vehicle navigation. Can machine learning enable similar leaps in the natural and social sciences? This is certainly the expectation in many scientiﬁc ﬁelds and recent years have seen a plethora of applications of non-linear models to a wide range of datasets. However, ﬂexible non-linear solutions will not always improve upon manually adding transforms and interactions between variables to linear regression models. We discuss how to recognize this before constructing a data-driven model and how such analysis can help us move to intrinsically interpretable regression models. Furthermore, for a variety of applications in the natural and social sciences we demonstrate why improvements may be seen with more complex regression models and why they may not.

Constructing Effective Machine Learning Models for the Sciences: A Multidisciplinary Perspective

The quantum Drude oscillator (QDO) is an efficient yet accurate coarse-grained approach that has been widely used to model electronic and optical response properties of atoms and molecules as well as polarization and dispersion interactions between them. Three effective parameters (frequency, mass, and charge) fully characterize the QDO Hamiltonian and are adjusted to reproduce response properties. However, the soaring success of coupled QDOs for many-atom systems remains fundamentally unexplained, and the optimal mapping between atoms/molecules and oscillators has not been established. Here we present an optimized parametrization (OQDO) where the parameters are fixed by using only dipolar properties. For the periodic table of elements as well as small molecules, our model accurately reproduces atomic (spatial) polarization potentials and multipolar dispersion coefficients, elucidating the high promise of the presented model in the development of next-generation quantum-mechanical force fields for (bio)molecular simulations.

https://pubs.acs.org/doi/pdf/10.1021/acs.jpclett.3c01221

Optimized Quantum Drude Oscillators for Atomic and Molecular Response Properties.

We combine the microcanonical formulation of lattice gauge theories (LGTs) developed by Callaway and the microcanonical inflection point analysis (MIPA) proposed by Bachmann et al. to achieve a systematic characterization of phase transitions (PTs) in U(1) lattice electrodynamics. Besides identifying the well-known deconfinement PT (DPT) due to the neutral pair dissolution, which we classify as a first-order PT, we unequivocally detect three higher-order PTs. According to MIPA, we observe two independent third-order PTs in the confined phase; instead, in the deconfined (Coulomb) phase, we observe a dependent third-order PT. For a deeper understanding of the physical meaning of these PTs, we numerically compute the average number density of monopolar and pair defects as a function of energy. Our analysis reveals that DPT is only one of the major mechanisms observable in LGT. The independent third-order PTs are associated, respectively, to the first occurrence of monopolar topological defects and to the production of pairs.

Alexandre Tkatchenko

Papers

Strong local-field enhancement of the nonlinear softmode response in aspirin

The three-center two-positron bond

Constructing Effective Machine Learning Models for the Sciences: A Multidisciplinary Perspective

Optimized Quantum Drude Oscillators for Atomic and Molecular Response Properties.

Phase Transitions in Abelian Lattice Gauge Theory: Production and Dissolution of Monopoles and Monopole-Antimonopole Pairs