Calculating Biological Behaviors of Epigenetic States in Phage lambda Life Cycle

Gene regulatory network of lambda phage is one the best studied model systems in molecular biology. More 50 years of experimental study has provided a tremendous amount of data at all levels: physics, chemistry, DNA, protein, and function. However, its stability and robustness for both wild type and mutants has been a notorious theoretical/mathematical problem. In this paper we report our successful calculation on the properties of this gene regulatory network. We believe it is of its first kind. Our success is of course built upon numerous previous theoretical attempts, but following 3 features make our modeling uniqu: 1) A new modeling method particular suitable for stability and robustness study; 2) Paying a close attention to the well-known difference of in vivo and in vitro; 3) Allowing more important role for noise and stochastic effect to play. The last two points have been discussed by two of us (Ao and Yin, cond-mat/0307747), which we believe would be enough to make some of previous theoretical attempts successful, too. We hope the present work would stimulate a further interest in the emerging field of gene regulatory network.Comment: 16 pages, 3 figures, 1 tabl

Non-locality in quantum field theory due to general relativity

We show that general relativity coupled to a quantum field theory generically leads to non-local effects in the matter sector. These non-local effects can be described by non-local higher dimensional operators which remarkably have an approximate shift symmetry. When applied to inflationary models, our results imply that small non-Gaussianities are a generic feature of models based on general relativity coupled to matter fields. However, these effects are too small to be observable in the cosmic microwave background

Stochastic Dynamical Structure (SDS) of Nonequilibrium Processes in the Absence of Detailed Balance. III: potential function in local stochastic dynamics and in steady state of Boltzmann-Gibbs type distribution function

From a logic point of view this is the third in the series to solve the problem of absence of detailed balance. This paper will be denoted as SDS III. The existence of a dynamical potential with both local and global meanings in general nonequilibrium processes has been controversial. Following an earlier explicit construction by one of us (Ao, J. Phys. {\bf A37}, L25 '04, arXiv:0803.4356, referred to as SDS II), in the present paper we show rigorously its existence for a generic class of situations in physical and biological sciences. The local dynamical meaning of this potential function is demonstrated via a special stochastic differential equation and its global steady-state meaning via a novel and explicit form of Fokker-Planck equation, the zero mass limit. We also give a procedure to obtain the special stochastic differential equation for any given Fokker-Planck equation. No detailed balance condition is required in our demonstration. For the first time we obtain here a formula to describe the noise induced shift in drift force comparing to the steady state distribution, a phenomenon extensively observed in numerical studies. The comparison to two well known stochastic integration methods, Ito and Stratonovich, are made ready. Such comparison was made elsewhere (Ao, Phys. Life Rev. {\bf 2} (2005) 117. q-bio/0605020).Comment: latex. 13 page

Simulation study on effect of chassis water cooling on solidification of eleven tons flat steel ingot

In this paper, the solidification process of eleven tons flat steel ingot is simulated by the finite element analysis software PROCAST, and the solidification state of the ingot with and without chassis is analyzed and compared. The results show that the forced cooling chassis makes low temperature area of the bottom ingot enlarged. And it has little influence on the temperature field and the solidification speed of the upper ingot. For the small flat steel ingot, the forced cooling chassis will deteriorate the shrinkage

Quantifying physical transport and local proliferation of phytoplankton downstream of an eutrophicated lake

Eutrophication in a freshwater system has mainly been studied in lakes and their upstream rivers, which are responsible to bring pollutants into the lakes. However, the influence of lakes on downstream rivers suffered massive algae from upstream lakes has not been fully studied. Our study area is Liangxi river, downstream of Taihu Lake, which is highly eutrophicated. The algae in Liangxi river has two origins: the physical transport from Taihu Lake and the in-situ proliferation. This paper aims to apply numerical model to quantify these two processes. The model is calibrated against the measured data in 2018. This computational condition that includes both algal processes is termed as Scheme A. Then, we regarded phytoplankton as a conservative substance by turning off the phytoplankton biological process and calculated term it as Scheme E. We selected the chl-a concentration in Hongqiao (LX2) section to represent the amount of algae in Liangxi river. The average chl-a difference in this section between Schemes A and E, Delta, can be used to quantify the magnitude of in-situ proliferation. The Delta varies seasonally, and the annual average is 7.22 mg/m³, which is 44.7% of the amount attributed to the physical transport. Liangxi river lies in an urban area which might encounter extreme events which to facilitate the in-situ proliferation, such as increased temperature and or excessive nutrient load. To quantify the level of algae under extreme situations, we design Schemes B, C and D which eliminated the limitation on algal growth by temperature, nitrogen and phosphorus respectively. Compared with the Scheme A, Schemes B, C and D oberve 21.8%, 65.7%and 61.2% respectively, increase in the average algal concentration. In the vertical direction, the chl-a concentration varies between 0.8mg/m³ and 2 mg/m³ in Scheme A, while the vertical concentration variances of chl-a in schemes B, C and D are found to be 5.56 mg/m³, 12.11 mg/m³ and 3.30 mg/m³, respectively.National Natural Science Foundation of China (No.51779075); Priority Academic Program Development of Jiangsu Higher Education Institutions; Major Science and Technology Program for Water Pollution Control and Treatment of China (2017ZX07203002-01)