Langevin Thermostat for Rigid Body Dynamics

We present a new method for isothermal rigid body simulations using the quaternion representation and Langevin dynamics. It can be combined with the traditional Langevin or gradient (Brownian) dynamics for the translational degrees of freedom to correctly sample the NVT distribution in a simulation of rigid molecules. We propose simple, quasi-symplectic second-order numerical integrators and test their performance on the TIP4P model of water. We also investigate the optimal choice of thermostat parameters.Comment: 15 pages, 13 figures, 1 tabl

New Langevin and Gradient Thermostats for Rigid Body Dynamics

We introduce two new thermostats, one of Langevin type and one of gradient (Brownian) type, for rigid body dynamics. We formulate rotation using the quaternion representation of angular coordinates; both thermostats preserve the unit length of quaternions. The Langevin thermostat also ensures that the conjugate angular momenta stay within the tangent space of the quaternion coordinates, as required by the Hamiltonian dynamics of rigid bodies. We have constructed three geometric numerical integrators for the Langevin thermostat and one for the gradient thermostat. The numerical integrators reflect key properties of the thermostats themselves. Namely, they all preserve the unit length of quaternions, automatically, without the need of a projection onto the unit sphere. The Langevin integrators also ensure that the angular momenta remain within the tangent space of the quaternion coordinates. The Langevin integrators are quasi-symplectic and of weak order two. The numerical method for the gradient thermostat is of weak order one. Its construction exploits ideas of Lie-group type integrators for differential equations on manifolds. We numerically compare the discretization errors of the Langevin integrators, as well as the efficiency of the gradient integrator compared to the Langevin ones when used in the simulation of rigid TIP4P water model with smoothly truncated electrostatic interactions. We observe that the gradient integrator is computationally less efficient than the Langevin integrators. We also compare the relative accuracy of the Langevin integrators in evaluating various static quantities and give recommendations as to the choice of an appropriate integrator.Comment: 16 pages, 4 figure

Climate change impact on thermal comfort in Mexico City housing

This is the author accepted manuscript. The final version is available from WEENTECH via the DOI in this record4th International Conference on Energy, Environment and Economics (ICEEE2019), 20-22 August 2019, Edinburgh, ScotlandA two storey terraced house was modelled in ESP-r with a simple window opening control strategy to represent typical dwellings found in Mexico City and the adjoining municipalities. Future weather data was generated for years in this century based on morphing methods developed from the literature and by the authors and a TMY weather file developed from historical data between 1975 to 1989 by WhiteBox Technologies. The population in the region under consideration is a little over 20 million which represents 16% of Mexico’s population. The present day climate is such that air conditioning is rarely used in single family housing. The main cooling strategy in the hottest months (Mid February to mid June) is window opening. This was modelled considering that if the interior temperature was at or above 18°C and the exterior air temperature was below the interior air temperature then windows would be open. The air flow was modelled using the flow network model within ESP-r. It was found that in the latter part of the present century, this strategy would become increasingly ineffective. This is likely to lead to a considerable increase in installed air conditioning in single family dwellings and a consequent increase in electricity demand and consumption leading to a need for substantial investments in electricity transmission and distribution systems in the region to bring in power from distant sources.Engineering and Physical Sciences Research Council (EPSRC)CONACYT-SENER-Sustentabilidad Energética fund Mexic

Two coupled feedback loops explain random mono-allelic Xist upregulation at the onset of X-chromosome inactivation

In female mammal s, dosage compensation for X-linked genes is ensured through random X-chromosome inactivation, which is initiated by mono-allelic up-regulation of Xist . We use mathematical modeling to identify the regulatory principles required to establish the mono-allelic and female-specific Xist expression pattern and test model predictions experimentally. A cis -acting positive feedback, which in mice is mediated by mutual repression of Xist and its antisense transcript Tsix , together with a trans -acting negative feedba ck are sufficient to explain mono-allelic Xist up-regulation. The model can reproduce data from several mutant, aneuploid and polyploid murine cell lines and explain s Xist expression patterns in other mammalian species. Furthermore, it predicts that transient , reversible bi-allelic Xist expression is not restricted to rabbits and humans but can also occur in mice, which we indeed confirm to occur in mouse embryos. Overall, our study provides a conceptual framework of the molecular mechanisms required to initiate random X-chromosome inactivation

The Two Active X Chromosomes in Female ESCs Block Exit from the Pluripotent State by Modulating the ESC Signaling Network

During early development of female mouse embryos, both X chromosomes are transiently active. X gene dosage is then equalized between the sexes through the process of X chromosome inactivation (XCI). Whether the double dose of X-linked genes in females compared with males leads to sex-specific developmental differences has remained unclear. Using embryonic stem cells with distinct sex chromosome compositions as a model system, we show that two X chromosomes stabilize the naive pluripotent state by inhibiting MAPK and Gsk3 signaling and stimulating the Akt pathway. Since MAPK signaling is required to exit the pluripotent state, differentiation is paused in female cells as long as both X chromosomes are active. By preventing XCI or triggering it precociously, we demonstrate that this differentiation block is released once XX cells have undergone X inactivation. We propose that double X dosage interferes with differentiation, thus ensuring a tight coupling between X chromosome dosage compensation and development

Cosmic No Hair for Collapsing Universes

It is shown that all contracting, spatially homogeneous, orthogonal Bianchi cosmologies that are sourced by an ultra-stiff fluid with an arbitrary and, in general, varying equation of state asymptote to the spatially flat and isotropic universe in the neighbourhood of the big crunch singularity. This result is employed to investigate the asymptotic dynamics of a collapsing Bianchi type IX universe sourced by a scalar field rolling down a steep, negative exponential potential. A toroidally compactified version of M*-theory that leads to such a potential is discussed and it is shown that the isotropic attractor solution for a collapsing Bianchi type IX universe is supersymmetric when interpreted in an eleven-dimensional context.Comment: Extended discussion to include Kantowski-Sachs universe. In press, Classical and Quantum Gravit

Measurements of Low Temperature Rate Coefficients for the Reaction of CH with CH₂O and Application to Dark Cloud and AGB Stellar Wind Models

Rate coefficients have been measured for the reaction of CH radicals with formaldehyde, CH₂O, over the temperature range of 31–133 K using a pulsed Laval nozzle apparatus combined with pulsed laser photolysis and laser-induced fluorescence spectroscopy. The rate coefficients are very large and display a distinct decrease with decreasing temperature below 70 K, although classical collision rate theory fails to reproduce this temperature dependence. The measured rate coefficients have been parameterized and used as input for astrochemical models for both dark cloud and Asymptotic Giant Branch stellar outflow scenarios. The models predict a distinct change (up to a factor of two) in the abundance of ketene, H₂CCO, which is the major expected molecular product of the CH + CH₂O reaction

Повернення в Ніжин (корпус документів з епістолярію І.Г. Спаського)

Підготовка до друку та переднє слово Наталії ДМИТРЕНКО (Ніжин), коментарі Сергія ЗОЗУЛІ (Київ–Ніжин): Уперше вводиться до наукового обігу корпус джерел з епістолярію українського та російського радянського історика-нумізмата, музейника І.Г. Спаського. Корпус джерел який містить кореспонденцію, отриману відомим науковцем від кореспондентів-ніжинців, і де, здебільшого, відображена “ніжинська тематика” – проблеми збереження культурної спадщини Ніжина, післявоєнного розвитку міста тощо.Подготовка к печати и предисловие Наталии ДМИТРЕНКО (Нежин), комментарии Сергея ЗОЗУЛИ (Киев–Нежин): Впервые вводится в научный оборот корпус источников из эпистолярия украинского и российского советского историка-нумизмата, музейщика И.Г. Спасского. Корпус источников содержит корреспонденцию, полученную известным ученым от корреспондентов-нежинцев, и в котором преимущественно отображена “нежинская тематика” – проблемы сохранения культурного наследия Нежина, послевоенного развития города и т.п.Preparation to the print and preface of Nataliya DMYTRENKO (Nizhyn), comments of Serhiy ZOZULYA (Kyiv–Nizhyn): The corps of sources from the epistolary legacy of the Ukrainian and Russian soviet historiannumismatist and museum worker I.G. Spas’kiy is entered to the scientific appeal in the first time. This corps of sources contains correspondence got the known scientist from Nizhynians and contains mostly “Nizhyn themes” – problems of protect of Nizhyn’s cultural legacy, post-war development of this town etc