Mitigating sign problem by automatic differentiation

As an intrinsically-unbiased method, quantum Monte Carlo (QMC) is of unique importance in simulating interacting quantum systems. Unfortunately, QMC often suffers from the notorious sign problem. Although generically curing sign problem is shown to be hard (NP-hard), sign problem of a given quantum model may be mitigated (sometimes even cured) by finding better choices of simulation scheme. A universal framework in identifying optimal QMC schemes has been desired. Here, we propose a general framework using automatic differentiation (AD) to automatically search for the best continuously-parameterized QMC scheme, which we call "automatic differentiable sign mitigation" (ADSM). We further apply the ADSM framework to the honeycomb lattice Hubbard model with Rashba spin-orbit coupling and demonstrate ADSM's effectiveness in mitigating its sign problem. For the model under study, ADSM leads a significant power-law acceleration in computation time (the computation time is reduced from $M$ to the order of $M^{\nu}$ with $\nu\approx 2/3$).Comment: 4.1 pages + supplemental materials, 4 figure

Asymptotic sign free in interacting fermion models

As an intrinsically-unbiased approach, quantum Monte Carlo (QMC) is of vital importance in understanding correlated phases of matter. Unfortunately, it often suffers notorious sign problem when simulating interacting fermion models. Here, we show for the first time that there exist interacting fermion models whose sign problem becomes less severe for larger system sizes and eventually disappears in the thermodynamic limit, which we dub as "asymptotic sign free". We demonstrate asymptotically-free sign in determinant QMC for various interacting models. Moreover, based on renormalization-group-like ideas we propose a heuristic understanding of the feature of asymptotic sign free. We believe that asymptotic sign free behavior could shed new lights to deepening our understanding of sign problem. More importantly, it can provide a promising way to decipher intriguing physics in correlated models which were conventionally thought not accessible by QMC.Comment: 4.5 pages plus supplemental material, 5 figure

Automatic Differentiable Monte Carlo: Theory and Application

Differentiable programming has emerged as a key programming paradigm empowering rapid developments of deep learning while its applications to important computational methods such as Monte Carlo remain largely unexplored. Here we present the general theory enabling infinite-order automatic differentiation on expectations computed by Monte Carlo with unnormalized probability distributions, which we call "automatic differentiable Monte Carlo" (ADMC). By implementing ADMC algorithms on computational graphs, one can also leverage state-of-the-art machine learning frameworks and techniques to traditional Monte Carlo applications in statistics and physics. We illustrate the versatility of ADMC by showing some applications: fast search of phase transitions and accurately finding ground states of interacting many-body models in two dimensions. ADMC paves a promising way to innovate Monte Carlo in various aspects to achieve higher accuracy and efficiency, e.g. easing or solving the sign problem of quantum many-body models through ADMC.Comment: 11.5 pages + supplemental materials, 4 figure

NGF-Induced Axon Growth Is Mediated by Localized Inactivation of GSK-3β and Functions of the Microtubule Plus End Binding Protein APC

Little is known about how nerve growth factor (NGF) signaling controls the regulated assembly of microtubules that underlies axon growth. Here we demonstrate that a tightly regulated and localized activation of phosphatidylinositol 3-kinase (PI3K) at the growth cone is essential for rapid axon growth induced by NGF. This spatially activated PI3K signaling is conveyed downstream through a localized inactivation of glycogen synthase kinase 3β (GSK-3β). These two spatially coupled kinases control axon growth via regulation of a microtubule plus end binding protein, adenomatous polyposis coli (APC). Our results demonstrate that NGF signals are transduced to the axon cytoskeleton via activation of a conserved cell polarity signaling pathway

A Thermostable β-Glucuronidase Obtained by Directed Evolution as a Reporter Gene in Transgenic Plants

A β-glucuronidase variant, GUS-TR3337, that was obtained by directed evolution exhibited higher thermostability than the wild-type enzyme, GUS-WT. In this study, the utility of GUS-TR337 as an improved reporter was evaluated. The corresponding gus-tr3337 and gus-wt genes were independently cloned in a plant expression vector and introduced into Arabidopsis thaliana. With 4-MUG as a substrate, plants containing the gus-wt gene showed no detectable β-glucuronidase activity after exposure to 60°C for 10 min, while those hosting the gus-tr3337 gene retained 70% or 50% activity after exposure to 80°C for 10 min or 30 min, respectively. Similarly, in vivo β-glucuronidase activity could be demonstrated by using X-GLUC as a substrate in transgenic Arabidopsis plants hosting the gus-tr3337 gene that were exposed to 80°C for up to 30 min. Thus, the thermostability of GUS-TR3337 can be exploited to distinguish between endogenous and transgenic β-glucuronidase activity, which is a welcome improvement in its use as a reporter

Current and future therapeutic strategies for Alzheimer’s disease: an overview of drug development bottlenecks

Alzheimer’s disease (AD) is the most common chronic neurodegenerative disease worldwide. It causes cognitive dysfunction, such as aphasia and agnosia, and mental symptoms, such as behavioral abnormalities; all of which place a significant psychological and economic burden on the patients’ families. No specific drugs are currently available for the treatment of AD, and the current drugs for AD only delay disease onset and progression. The pathophysiological basis of AD involves abnormal deposition of beta-amyloid protein (Aβ), abnormal tau protein phosphorylation, decreased activity of acetylcholine content, glutamate toxicity, autophagy, inflammatory reactions, mitochondria-targeting, and multi-targets. The US Food and Drug Administration (FDA) has approved five drugs for clinical use: tacrine, donepezil, carbalatine, galantamine, memantine, and lecanemab. We have focused on the newer drugs that have undergone clinical trials, most of which have not been successful as a result of excessive clinical side effects or poor efficacy. Although aducanumab received rapid approval from the FDA on 7 June 2021, its long-term safety and tolerability require further monitoring and confirmation. In this literature review, we aimed to explore the possible pathophysiological mechanisms underlying the occurrence and development of AD. We focused on anti-Aβ and anti-tau drugs, mitochondria-targeting and multi-targets, commercially available drugs, bottlenecks encountered in drug development, and the possible targets and therapeutic strategies for future drug development. We hope to present new concepts and methods for future drug therapies for AD

Neurotrophins support regenerative axon assembly over CSPGs by an ECM-integrin-independent mechanism

Chondroitin sulfate proteoglycans (CSPGs) and myelin-based inhibitors are the most studied inhibitory molecules in the adult central nervous system. Unlike myelin-based inhibitors, few studies have reported ways to overcome the inhibitory effect of CSPGs. Here, by using regenerating adult dorsal root ganglion (DRG) neurons, we show that chondroitin sulfate proteoglycans inhibit axon assembly by a different mechanism from myelin-based inhibitors. Furthermore, we show that neither Rho inhibition nor cAMP elevation rescues extracellular factor-induced axon assembly inhibited by CSPGs. Instead, our data suggest that CSPGs block axon assembly by interfering with integrin signaling. Surprisingly, we find that nerve growth factor (NGF) promotes robust axon growth of regenerating DRG neurons over CSPGs. We have found that, unlike naive neurons that require simultaneous activation of neurotrophin and integrin pathways for axon assembly, either neurotrophin or integrin signaling alone is sufficient to induce axon assembly of regenerating neurons. Thus, our results suggest that the ability of NGF to overcome CSPG inhibition in regenerating neurons is probably due to the ability of regenerating neurons to assemble axons using an integrin-independent pathway. Finally, our data show that the GSK-3beta-APC pathway, previously shown to mediate developing axon growth, is also necessary for axon regeneration

Anti-HCV reactive volunteer blood donors distribution character and genotypes switch in Xi'an, China

HCV is prevailed in the world as well as in China. Blood transfusion is one of the most common transmission pathways of this pathogen. Although data of HCV infection character were reported during the past years, anti-HCV reactive profile of China donors was not fully clear yet. Furthermore, infection progress was found related to the HCV genotype. Different genotype led to different efficacy when interferon was introduced into HCV therapy. Here we provided character data of HCV infection in China blood donors from the year of 2000 to 2009. The infection rate in local donors was lower than general population and descended from 0.80% to 0.40% or so in recent years. About 83% HCV strains were categorized into genotypes 1b and 2a. But 1b subtype cases climbed and 2a subtype cases decreased. The current study threw more light on HCV infection of blood donors in China, at least in the Northern region