Bayesian selection for coarse-grained models of liquid water

The necessity for accurate and computationally efficient representations of water in atomistic simulations that can span biologically relevant timescales has born the necessity of coarse-grained (CG) modeling. Despite numerous advances, CG water models rely mostly on a-priori specified assumptions. How these assumptions affect the model accuracy, efficiency, and in particular transferability, has not been systematically investigated. Here we propose a data driven, comparison and selection for CG water models through a Hierarchical Bayesian framework. We examine CG water models that differ in their level of coarse-graining, structure, and number of interaction sites. We find that the importance of electrostatic interactions for the physical system under consideration is a dominant criterion for the model selection. Multi-site models are favored, unless the effects of water in electrostatic screening are not relevant, in which case the single site model is preferred due to its computational savings. The charge distribution is found to play an important role in the multi-site model's accuracy while the flexibility of the bonds/angles may only slightly improve the models. Furthermore, we find significant variations in the computational cost of these models. We present a data informed rationale for the selection of CG water models and provide guidance for future water model designs

Stability Analysis and Stabilization Strategies for Linear Supply Chains

Due to delays in the adaptation of production or delivery rates, supply chains can be dynamically unstable with respect to perturbations in the consumption rate, which is known as "bull-whip effect". Here, we study several conceivable production strategies to stabilize supply chains, which is expressed by different specifications of the management function controlling the production speed in dependence of the stock levels. In particular, we will investigate, whether the reaction to stock levels of other producers or suppliers has a stabilizing effect. We will also demonstrate that the anticipation of future stock levels can stabilize the supply system, given the forecast horizon is long enough. To show this, we derive linear stability conditions and carry out simulations for different control strategies. The results indicate that the linear stability analysis is a helpful tool for the judgement of the stabilization effect, although unexpected deviations can occur in the non-linear regime. There are also signs of phase transitions and chaotic behavior, but this remains to be investigated more thoroughly in the future.Comment: For related work see http://www.helbing.or

Accurate machine learning force fields via experimental and simulation data fusion

Machine Learning (ML)-based force fields are attracting ever-increasing interest due to their capacity to span spatiotemporal scales of classical interatomic potentials at quantum-level accuracy. They can be trained based on high-fidelity simulations or experiments, the former being the common case. However, both approaches are impaired by scarce and erroneous data resulting in models that either do not agree with well-known experimental observations or are under-constrained and only reproduce some properties. Here we leverage both Density Functional Theory (DFT) calculations and experimentally measured mechanical properties and lattice parameters to train an ML potential of titanium. We demonstrate that the fused data learning strategy can concurrently satisfy all target objectives, thus resulting in a molecular model of higher accuracy compared to the models trained with a single data source. The inaccuracies of DFT functionals at target experimental properties were corrected, while the investigated off-target properties remained largely unperturbed. Our approach is applicable to any material and can serve as a general strategy to obtain highly accurate ML potentials

Learning neural network potentials from experimental data via Differentiable Trajectory Reweighting

In molecular dynamics (MD), neural network (NN) potentials trained bottom-up on quantum mechanical data have seen tremendous success recently. Top-down approaches that learn NN potentials directly from experimental data have received less attention, typically facing numerical and computational challenges when backpropagating through MD simulations. We present the Differentiable Trajectory Reweighting (DiffTRe) method, which bypasses differentiation through the MD simulation for time-independent observables. Leveraging thermodynamic perturbation theory, we avoid exploding gradients and achieve around 2 orders of magnitude speed-up in gradient computation for top-down learning. We show effectiveness of DiffTRe in learning NN potentials for an atomistic model of diamond and a coarse-grained model of water based on diverse experimental observables including thermodynamic, structural and mechanical properties. Importantly, DiffTRe also generalizes bottom-up structural coarse-graining methods such as iterative Boltzmann inversion to arbitrary potentials. The presented method constitutes an important milestone towards enriching NN potentials with experimental data, particularly when accurate bottom-up data is unavailable.Comment: This is a post-peer-review, pre-copyedit version of an article published in Nature Communications. The final authenticated version is available online at: http://dx.doi.org/10.1038/s41467-021-27241-

Modeling Supply Networks and Business Cycles as Unstable Transport Phenomena

Physical concepts developed to describe instabilities in traffic flows can be generalized in a way that allows one to understand the well-known instability of supply chains (the so-called ``bullwhip effect''). That is, small variations in the consumption rate can cause large variations in the production rate of companies generating the requested product. Interestingly, the resulting oscillations have characteristic frequencies which are considerably lower than the variations in the consumption rate. This suggests that instabilities of supply chains may be the reason for the existence of business cycles. At the same time, we establish some link to queuing theory and between micro- and macroeconomics.Comment: For related work see http://www.helbing.or

Order and interactions in DNA arrays: Multiscale molecular dynamics simulation

While densely packed DNA arrays are known to exhibit hexagonal and orthorhombic local packings, the detailed mechanism governing the associated phase transition remains rather elusive. Furthermore, at high densities the atomistic resolution is paramount to properly account for fine details, encompassing the DNA molecular order, the contingent ordering of counterions and the induced molecular ordering of the bathing solvent, bringing together electrostatic, steric, thermal and direct hydrogen-bonding interactions, resulting in the observed osmotic equation of state. We perform a multiscale simulation of dense DNA arrays by enclosing a set of 16 atomistically resolved DNA molecules within a semi-permeable membrane, allowing the passage of water and salt ions, and thus mimicking the behavior of DNA arrays subjected to external osmotic stress in a bathing solution of monovalent salt and multivalent counterions. By varying the DNA density, local packing symmetry, and counterion type, we obtain osmotic equation of state together with the hexagonal-orthorhombic phase transition, and full structural characterization of the DNA subphase in terms of its positional and angular orientational fluctuations, counterion distributions, and the solvent local dielectric response profile with its order parameters that allow us to identify the hydration force as the primary interaction mechanism at high DNA densities.ISSN:2045-232

NURSING CARE OF STROKE PATIENT

Cerebrovaskularne bolesti, bolesti moždanih krvnih žila, predstavljaju danas jedan od najvećih problema suvremenog čovječanstva. Moždani udar, kao najznačajniji predstavnik, treći je uzrok smrtnosti, a prvi uzrok invaliditeta u svijetu. Moždani udar je akutno stanje koje je uzrokovano oštećenjem moždanih struktura okluzijom arterija s posljedičnom ishemijom pripadajućeg područja krvne žile ili stanje nastalo zbog prsnuća krvne žile sa izljevom u moždani parenhim. S obzirom na patofiziološke procese dijelimo ga na ishemijski i hemoragijski, a s obzirom na vrijeme trajanja dijelimo ga na TIA-u, RIND, progresivni moždani udar ili potpuni moždani udar. Simptomi moždanog udara su: smetnje vida u smislu nejasnog vida te pojava dvoslika, trnjenje usana, jezika ili jedne polovice lica i tijela, smetnje govora u smislu poteškoća pri izgovaranju ili razumijevanju govora. motorni deficit s gubitkom snage u jednoj nozi ili ruci ili jednoj polovici tijela, zbunjeno i smeteno stanje, iznenadna jaka glavobolja, dezorijentacija u vremenu i prostoru te promjena stanja svijesti. Zdravstvena njega bolesnika s moždani udarom prvenstveno je usmjerena na otkrivanje i djelovanje na čimbenike rizika moždanog udara, a potom na očuvanje preostalih sposobnosti nakon moždanog udara te na osposobljavanje, najprije, za aktivnosti samozbrinjavanja, a onda i na zadovoljavanje ostalih ljudskih potreba. Primjenom procesa zdravstvene njege postiže se sustavno i dokumentirano praćenje zdravstvene njege bolesnika s moždanim udarom. U ovom radu je ukratko prikazana utvrđena potreba za zdravstvenom njegom, planiranje, provođenje i evaluacija zdravstvene njege s naglaskom na specifičnost zdravstvene njege bolesnika s moždanim udarom.A cerebrovascular diseases, the diseases of the blood vessels, represent today one of the biggest problem of a mankind. The stroke, as one of the most significant representative, is third cause of dead, and the first cause of disability in the world. A stroke is an acute condition which is caused by damage of brain structures following arterial occlusion with subsequent ischemia of respective territories or situation created due to the rupture of blood vessels with hemorrhage into the brain parenchyma. Given the pathophysiological processes work took him to ischemic and hemorrhagic, and given the time and duration divided by TIA, RIND, progressive stroke and complete stroke. Symptoms of stroke include: Vision problems in terms of vague vision or double vision, numbness of the lips, tongue, or one half of the face and body, annoyance speech in terms of difficulty in pronunciation or understanding speech, power deficit with the loss of power in one arm, leg or one half of the body, confused and disoriented state, sudden severe headache especially if it has not occurred, disorientation to time and place and altered mental status. The health care of the stroke victim is direct on the revealing and activity on the risk factors of the stroke and also on the caring of the other abilities after the stroke and also on the capability, in the first place, for the activities of the self care and then on the satisfaction of the other human needs. Application of the process of the nursing care, we can achieve systematic and documented monitoring of the nursing care of stroke victim. In this work, it's shortly presented the confirmation of the needs for the nursing care, planning, leading and evaluation of the nursing care with an accent on the specifics of the nursing care of the stroke victim

SWINGER:A clustering algorithm for concurrent coupling of atomistic and supramolecular liquids

In this contribution, we review recent developments and applications of a dynamic clustering algorithm SWINGER tailored for the multiscale molecular simulations of biomolecular systems. The algorithm on-the-fly redistributes solvent molecules among supramolecular clusters. In particular, we focus on its applications in combination with the adaptive resolution scheme, which concurrently couples atomistic and coarse-grained molecular representations. We showcase the versatility of our multiscale approach on a few applications to biomolecular systems coupling atomistic and supramolecular water models such as the well-established MARTINI and dissipative particle dynamics models and provide an outlook for future work

NURSING CARE OF STROKE PATIENT

Cerebrovaskularne bolesti, bolesti moždanih krvnih žila, predstavljaju danas jedan od najvećih problema suvremenog čovječanstva. Moždani udar, kao najznačajniji predstavnik, treći je uzrok smrtnosti, a prvi uzrok invaliditeta u svijetu. Moždani udar je akutno stanje koje je uzrokovano oštećenjem moždanih struktura okluzijom arterija s posljedičnom ishemijom pripadajućeg područja krvne žile ili stanje nastalo zbog prsnuća krvne žile sa izljevom u moždani parenhim. S obzirom na patofiziološke procese dijelimo ga na ishemijski i hemoragijski, a s obzirom na vrijeme trajanja dijelimo ga na TIA-u, RIND, progresivni moždani udar ili potpuni moždani udar. Simptomi moždanog udara su: smetnje vida u smislu nejasnog vida te pojava dvoslika, trnjenje usana, jezika ili jedne polovice lica i tijela, smetnje govora u smislu poteškoća pri izgovaranju ili razumijevanju govora. motorni deficit s gubitkom snage u jednoj nozi ili ruci ili jednoj polovici tijela, zbunjeno i smeteno stanje, iznenadna jaka glavobolja, dezorijentacija u vremenu i prostoru te promjena stanja svijesti. Zdravstvena njega bolesnika s moždani udarom prvenstveno je usmjerena na otkrivanje i djelovanje na čimbenike rizika moždanog udara, a potom na očuvanje preostalih sposobnosti nakon moždanog udara te na osposobljavanje, najprije, za aktivnosti samozbrinjavanja, a onda i na zadovoljavanje ostalih ljudskih potreba. Primjenom procesa zdravstvene njege postiže se sustavno i dokumentirano praćenje zdravstvene njege bolesnika s moždanim udarom. U ovom radu je ukratko prikazana utvrđena potreba za zdravstvenom njegom, planiranje, provođenje i evaluacija zdravstvene njege s naglaskom na specifičnost zdravstvene njege bolesnika s moždanim udarom.A cerebrovascular diseases, the diseases of the blood vessels, represent today one of the biggest problem of a mankind. The stroke, as one of the most significant representative, is third cause of dead, and the first cause of disability in the world. A stroke is an acute condition which is caused by damage of brain structures following arterial occlusion with subsequent ischemia of respective territories or situation created due to the rupture of blood vessels with hemorrhage into the brain parenchyma. Given the pathophysiological processes work took him to ischemic and hemorrhagic, and given the time and duration divided by TIA, RIND, progressive stroke and complete stroke. Symptoms of stroke include: Vision problems in terms of vague vision or double vision, numbness of the lips, tongue, or one half of the face and body, annoyance speech in terms of difficulty in pronunciation or understanding speech, power deficit with the loss of power in one arm, leg or one half of the body, confused and disoriented state, sudden severe headache especially if it has not occurred, disorientation to time and place and altered mental status. The health care of the stroke victim is direct on the revealing and activity on the risk factors of the stroke and also on the caring of the other abilities after the stroke and also on the capability, in the first place, for the activities of the self care and then on the satisfaction of the other human needs. Application of the process of the nursing care, we can achieve systematic and documented monitoring of the nursing care of stroke victim. In this work, it's shortly presented the confirmation of the needs for the nursing care, planning, leading and evaluation of the nursing care with an accent on the specifics of the nursing care of the stroke victim

Adaptive resolution simulation of an atomistic DNA molecule in MARTINI salt solution

We present a dual-resolution model of a deoxyribonucleic acid (DNA) molecule in a bathing solution, where we concurrently couple atomistic bundled water and ions with the coarse-grained MAR- TINI model of the solvent. We use our fine-grained salt solution model as a solvent in the inner shell surrounding the DNA molecule, whereas the solvent in the outer shell is modeled by the coarse-grained model. The solvent entities can exchange between the two domains and adapt their resolution accordingly. We critically asses the performance of our multiscale model in adaptive resolution simulations of an infinitely long DNA molecule, focusing on the structural characteristics of the solvent around DNA. Our analysis shows that the adaptive resolution scheme does not produce any noticeable artifacts in comparison to a refer- ence system simulated in full detail. The effect of using a bundled-SPC model, required for multiscaling, compared to the standard free SPC model is also evaluated. Our multiscale approach opens the way for large scale applications of DNA and other biomolecules which require a large solvent reservoir to avoid boundary effects