Getting excited: Challenges in quantum-classical studies of excitons in polymeric systems

A combination of classical molecular dynamics (MM/MD) and quantum chemical calculations based on the density functional theory (DFT) was performed to describe conformational properties of diphenylethyne (DPE), methylated-DPE and poly para phenylene ethynylene (PPE). DFT calculations were employed to improve and develop force field parameters for MM/MD simulations. Many-body Green's functions theory within the GW approximation and the Bethe-Salpeter equation were utilized to describe excited states of the systems. Reliability of the excitation energies based on the MM/MD conformations was examined and compared to the excitation energies from DFT conformations. The results show an overall agreement between the optical excitations based on MM/MD conformations and DFT conformations. This allows for calculation of excitation energies based on MM/MD conformations

Morphology of Proliferating Epithelial Cellular Tissue

We investigate morphologies of proliferating cellular tissue using a newly developed numerical simulation model for mechanical cell division. The model reproduces structures of simple multi-cellular organisms via simple rules for selective division and division plane orientation. The model is applied to a bimodal mixture of stiff cells with a low growth potential and soft cells with a high growth potential. In an even mixture, the soft cells develop into a tissue matrix and the stiff cells into a dendrite-like network structure. For soft cell inclusion in a stiff cellular matrix, the soft cells develop to a fast growing tumour like structure that gradually evacuates the stiff cell matrix. With increasing inter-cell friction, the tumour growth slows down and parts of it is driven to self-inflicted cell death

A Kernel-based Machine Learning Approach to Computing Quasiparticle Energies within Many-Body Green's Functions Theory

We present a Kernel Ridge Regression (KRR) based supervised learning method combined with Genetic Algorithms (GAs) for the calculation of quasiparticle energies within Many-Body Green's Functions Theory. These energies representing electronic excitations of a material are solutions to a set of non-linear equations, containing the electron self-energy (SE) in the $GW$ approximation. Due to the frequency-dependence of this SE, standard approaches are computationally expensive and may yield non-physical solutions, in particular for larger systems. In our proposed model, we use KRR as a self-adaptive surrogate model which reduces the number of explicit calculations of the SE. Transforming the standard fixed-point problem of finding quasiparticle energies into a global optimization problem with a suitably defined fitness function, application of the GA yields uniquely the physically relevant solution. We demonstrate the applicability of our method for a set of molecules from the $GW$100 dataset, which are known to exhibit a particularly problematic structure of the SE. Results of the KRR-GA model agree within less than 0.01 eV with the reference standard implementation, while reducing the number of required SE evaluations roughly by a factor of ten.Comment: 4 pages, 3 figures, conference: Machine Learning for Molecules Workshop at NeurIPS 202

Jamming and force distribution in growing epithelial tissue

We investigate morphologies of proliferating cellular tissues using a newly developed numerical simulation model for mechanical cell division and migration in 2D. The model is applied to a bimodal mixture consisting of stiff cells with a low growth potential and soft cells with a high growth potential; cancer cells are typically considered to be softer than healthy cells. In an even mixture, the soft cells develop into a tissue matrix and the stiff cells into a dendrite-like network structure. When soft cells are placed inside a tissue consisting of stiff cells (to model cancer growth), the soft cells develop to a fast growing tumor-like structure that gradually evacuates the stiff cell matrix. The model also demonstrates 1) how soft cells orient themselves in the direction of the largest effective stiffness as predicted by the theory of Bischofs and Schwarz (Proc. Natl. Acad. Sci U.S.A., 100, 9274--9279 (2003) and 2) that the orientation and force generation continue a few cell rows behind the soft-stiff interface. With increasing inter-cell friction, tumor growth slows down and cell death occurs. The contact force distribution between cells is demonstrated to be highly sensitive to cell type mixtures and cell-cell interactions, which indicates that local mechanical forces can be useful as a regulator of tissue formation. The results shed new light on established experimental data.Comment: arXiv admin note: text overlap with arXiv:1811.0757

Glassy dynamics from generalized mode-coupling theory: existence and uniqueness of solutions for hierarchically coupled integro-differential equations

Generalized mode-coupling theory (GMCT) is a first-principles-based and systematically correctable framework to predict the complex relaxation dynamics of glass-forming materials. The formal theory amounts to a hierarchy of infinitely many coupled integro-differential equations, which may be approximated using a suitable finite-order closure relation. Although previous studies have suggested that finite-order GMCT leads to well-defined solutions, and that the hierarchy converges as the closure level increases, no rigorous and general result in this direction is known. Here we unambiguously establish the existence and uniqueness of solutions to generic, schematic GMCT hierarchies that are closed at arbitrary order. We consider two types of commonly invoked closure approximations, namely mean-field and exponential closures. We also distinguish explicitly between overdamped and underdamped glassy dynamics, corresponding to hierarchies of first-order and second-order integro-differential equations, respectively. We find that truncated GMCT hierarchies closed under an exponential closure conform to previously developed mathematical theories, such that the existence of a unique solution can be readily inferred. Self-consistent mean-field closures, however, of which the well-known standard-MCT closure approximation is a special case, warrant additional arguments for mathematical rigour. We demonstrate that the existence of a priori bounds on the solution is sufficient to also prove that unique solutions exist for such self-consistent hierarchies. To complete our analysis, we present simple arguments to show that these a priori bounds must exist, motivated by the physical interpretation of the GMCT solutions as density correlation functions. Overall, our work contributes to the theoretical justification of GMCT for studies of the glass transition, placing GMCT on a firmer mathematical footing.Comment: 7 pages Revised version that contains minor changes and, in Sec. V, a revised argument. The former Sec. VI was suppressed and replaced by a more stringent bound derived now in Sec.

Electronic Excitations in Complex Molecular Environments: Many-Body Green's Functions Theory in VOTCA-XTP

Many-body Green's functions theory within the GW approximation and the Bethe-Salpeter Equation (BSE) is implemented in the open-source VOTCA-XTP software, aiming at the calculation of electronically excited states in complex molecular environments. Based on Gaussian-type atomic orbitals and making use of resolution of identify techniques, the code is designed specifically for non-periodic systems. Application to the small molecule reference set successfully validates the methodology and its implementation for a variety of excitation types covering an energy range from 2-8 eV in single molecules. Further, embedding each GW-BSE calculation into an atomistically resolved surrounding, typically obtained from Molecular Dynamics, accounts for effects originating from local fields and polarization. Using aqueous DNA as a prototypical system, different levels of electrostatic coupling between the regions in this GW-BSE/MM setup are demonstrated. Particular attention is paid to charge-transfer (CT) excitations in adenine base pairs. It is found that their energy is extremely sensitive to the specific environment and to polarization effects. The calculated redshift of the CT excitation energy compared to a nucelobase dimer treated in vacuum is of the order of 1 eV, which matches expectations from experimental data. Predicted lowest CT energies are below that of a single nucleobase excitation, indicating the possibility of an initial (fast) decay of such an UV excited state into a bi-nucleobase CT exciton. The results show that VOTCA-XTP's GW-BSE/MM is a powerful tool to study a wide range of types of electronic excitations in complex molecular environments