Cryo-EM map interpretation and protein model-building using iterative map segmentation.

A procedure for building protein chains into maps produced by single-particle electron cryo-microscopy (cryo-EM) is described. The procedure is similar to the way an experienced structural biologist might analyze a map, focusing first on secondary structure elements such as helices and sheets, then varying the contour level to identify connections between these elements. Since the high density in a map typically follows the main-chain of the protein, the main-chain connection between secondary structure elements can often be identified as the unbranched path between them with the highest minimum value along the path. This chain-tracing procedure is then combined with finding side-chain positions based on the presence of density extending away from the main path of the chain, allowing generation of a Cα model. The Cα model is converted to an all-atom model and is refined against the map. We show that this procedure is as effective as other existing methods for interpretation of cryo-EM maps and that it is considerably faster and produces models with fewer chain breaks than our previous methods that were based on approaches developed for crystallographic maps

\v{C}ech-Delaunay gradient flow and homology inference for self-maps

We call a continuous self-map that reveals itself through a discrete set of point-value pairs a sampled dynamical system. Capturing the available information with chain maps on Delaunay complexes, we use persistent homology to quantify the evidence of recurrent behavior. We establish a sampling theorem to recover the eigenspace of the endomorphism on homology induced by the self-map. Using a combinatorial gradient flow arising from the discrete Morse theory for \v{C}ech and Delaunay complexes, we construct a chain map to transform the problem from the natural but expensive \v{C}ech complexes to the computationally efficient Delaunay triangulations. The fast chain map algorithm has applications beyond dynamical systems.Comment: 22 pages, 8 figure

Uni-directional transport properties of a serpent billiard

We present a dynamical analysis of a classical billiard chain -- a channel with parallel semi-circular walls, which can serve as a model for a bended optical fiber. An interesting feature of this model is the fact that the phase space separates into two disjoint invariant components corresponding to the left and right uni-directional motions. Dynamics is decomposed into the jump map -- a Poincare map between the two ends of a basic cell, and the time function -- traveling time across a basic cell of a point on a surface of section. The jump map has a mixed phase space where the relative sizes of the regular and chaotic components depend on the width of the channel. For a suitable value of this parameter we can have almost fully chaotic phase space. We have studied numerically the Lyapunov exponents, time auto-correlation functions and diffusion of particles along the chain. As a result of a singularity of the time function we obtain marginally-normal diffusion after we subtract the average drift. The last result is also supported by some analytical arguments.Comment: 15 pages, 9 figure (19 .(e)ps files

Low-temperature thermodynamics for a flat-band ferromagnet: Rigorous versus numerical results

The repulsive Hubbard model on a sawtooth chain exhibits a lowest single-electron band which is completely dispersionless (flat) for a specific choice of the hopping parameters. We construct exact many-electron ground states for electron fillings up to 1/4. We map the low-energy degrees of freedom of the electron model to a model of classical hard dimers on a chain and, as a result, obtain the ground-state degeneracy as well as closed-form expressions for the low-temperature thermodynamic quantities around a particular value of the chemical potential. We compare our analytical findings with complementary numerical data. Although we consider a specific model, we believe that some of our results like a low-temperature peak in the specific heat are generic for flat-band ferromagnets.Comment: 5 pages, 1 figure; accepted for publication as a Rapid Communication in Physical Review

Optimal control of continuous-time Markov chains with noise-free observation

We consider an infinite horizon optimal control problem for a continuous-time Markov chain $X$ in a finite set $I$ with noise-free partial observation. The observation process is defined as $Y_t = h(X_t)$, $t \geq 0$, where $h$ is a given map defined on $I$. The observation is noise-free in the sense that the only source of randomness is the process $X$ itself. The aim is to minimize a discounted cost functional and study the associated value function $V$. After transforming the control problem with partial observation into one with complete observation (the separated problem) using filtering equations, we provide a link between the value function $v$ associated to the latter control problem and the original value function $V$. Then, we present two different characterizations of $v$ (and indirectly of $V$): on one hand as the unique fixed point of a suitably defined contraction mapping and on the other hand as the unique constrained viscosity solution (in the sense of Soner) of a HJB integro-differential equation. Under suitable assumptions, we finally prove the existence of an optimal control

Perancangan Peta Jalan Pengembangunan Industri Hasil Pertanian Pada Wilayah Kabupaten Dengan Metode VRISA Dan Rantai Nilai

.Industry development is an alternative in social welfare improvement of a region. This research was conducted to develop a road map of industry development in Kabupaten Bengkayang, West Kalimantan. VRISA (Value, Rare, In-imitabillity, Substitutability and Appropriability) framework used to determine appropriate industrial products to be developed. Based on value chain method, the development strategy was constructed into main value chain and supporting value chain strategy. Output of analysis showed that corn-based product was preferred by VRISA framework, so it needs to be developed as appropriate industry for Kabupaten Bengkayang. There are three stages of industrial development in the corn-based industry, namely initial phase (basic foundation establishment), main phase (implementation), and final stage (harvesting). Time frame for all stages takes five years

Aubry transition studied by direct evaluation of the modulation functions of infinite incommensurate systems

Incommensurate structures can be described by the Frenkel Kontorova model. Aubry has shown that, at a critical value K_c of the coupling of the harmonic chain to an incommensurate periodic potential, the system displays the analyticity breaking transition between a sliding and pinned state. The ground state equations coincide with the standard map in non-linear dynamics, with smooth or chaotic orbits below and above K_c respectively. For the standard map, Greene and MacKay have calculated the value K_c=.971635. Conversely, evaluations based on the analyticity breaking of the modulation function have been performed for high commensurate approximants. Here we show how the modulation function of the infinite system can be calculated without using approximants but by Taylor expansions of increasing order. This approach leads to a value K_c'=.97978, implying the existence of a golden invariant circle up to K_c' > K_c.Comment: 7 pages, 5 figures, file 'epl.cls' necessary for compilation provided; Revised version, accepted for publication in Europhysics Letter

Spin Gap of S=1/2 Heisenberg Model on Distorted Diamond Chain

We study the spin gap of the S=1/2 Heisenberg model on the distorted diamond chain, which is recently proposed to represent magnetic properties of Cu_3 Cl_6 (H_2 O)_2 2H_8 C_4 SO_2. This model is composed of stacked trimers and has three kinds of exchange interactions J_1, J_2 and J_3. Using the numerical diagonalization, we obtain a contour map of the spin gap in the J_2/J_1-J_3/J_1 plane. We argue possible values of the exchange constants based on the contour map and the observed value of the spin gap.Comment: 2 pages, 4 figure

Organic produce Value Chain Analysis (OF0344)

Growth in the Organic food market has been rapid in recent years. According to the soil association, retail sales of organic food are now worth £1.2 billion – an 11% increase on the previous year. Organic Supply Chains have developed to serve different routes to the consumer. Some chains are simple and involve direct supply to the consumer through, for example, box schemes and farmer’s markets. However in the main greater complexity is involved. Some 75% of organic food is sold through the multiple retailers. Generally speaking, this introduces more stages into the supply chain and as a result there is more complexity. All organic businesses have to be profitable and this requires them to operate efficiently. The Food Chain Centre has undertaken three projects dealing with organic producers supplying through multiple retailers. The projects applied the concept of ‘lean thinking’ and ‘value chain analysis’. The projects were led by the Food Process Innovation Unit, which is part of Cardiff University’s Lean Enterprise Research Centre. The Lean Enterprise Research Centre enjoys a global reputation in the application of lean thinking and their work demonstrates that businesses can use the concept to secure long term competitive advantage. Lean thinking provides a way to do more and more with less and less – less human effort, less equipment, less time, and less space – while coming closer and closer to providing consumers with exactly what they want. In other words, the project focused on removing waste from supply chains and focusing on customer value. This is an established approach based on practices first developed in the Japanese motor industry. Lean thinking has become widespread in UK manufacturing and according to a recent survey by McKinsey it is what sets apart the best performing manufacturers. Many companies that have embraced lean thinking have delivered dramatic improvements over a three year period including: • 90% reduction in defects • 90& reduction in response time to customer orders • 75% reduction in inventory • 50% reduction in space • 50% reduction in variable costs Organic production has some unique features that challenge the lean approach. These include: • The ethical underpinning for many businesses involved in organic production • The highly regulated nature of production that prohibits many practices prevalent in conventional food production • The small scale nature of a substantial part of organic production • The environmental factor – in that organic farming also makes a major contribution to higher levels of bio-diversity and lower levels of pollution The Cardiff team are not typical consultants, neither are they experts in organic production. They are expert facilitators, guiding teams drawn from businesses and helping them to see their supply chains in new light. Each project starts from a recognisable product that consumers purchase. The three projects deal with organic carrots, potatoes and lamb. In each case more than one business is involved in getting the product to market. The project constructed a team with members drawn from each business within the supply chain and support from Cardiff University facilitators to draw a ‘process map’ of the current state of affairs, making sure to capture what is actually happening (‘warts and all’) and not what is supposed to happen. The Cardiff team then helped each project team to investigate issues such as: • Do products flow through the chain as quickly as possible or are there unnecessary hold-ups? • Do some activities add more costs than value? In which case what can be done about it? In particular, are there activities that add absolutely no value to the consumer that can just be eliminated? • Have people learned to live with errors, treating them as inevitable or are they constantly striving to eliminate them? • Are the right quality tests in the right place in the chain and are they working effectively? • Are the right performance measures in place? • When problems are identified, are they traced to their source and dealt with? • Is the right information shared along the chain? • Are there effective ordering and stock holding policies that impose heavy costs on suppliers? The team then created a second map of how they would like the chain to operate in the future. Finally, they draw up an action plan of how to work in partnership to get there. The projects discovered that there were substantial opportunities to transform the profitability of business within the supply chain, whilst maintaining or improving customer value. These improvement opportunities include: • Re-designing the layout of factory and farm • Creating supply chain teams to focus on reducing faults at particular stages of the supply chain • Forums for customers and suppliers to work jointly on improvement projects • Agreeing to exchange information that is currently unavailable in a practical format • Collecting new performance measures and sharing these more widely • Making better use of Information Technology to share information • Working in partnership, to increase long term commitment to supply chain objective

Mapping domain characteristics influencing Analytics initiatives: The example of Supply Chain Analytics

Purpose: Analytics research is increasingly divided by the domains Analytics is applied to. Literature offers little understanding whether aspects such as success factors, barriers and management of Analytics must be investigated domain-specific, while the execution of Analytics initiatives is similar across domains and similar issues occur. This article investigates characteristics of the execution of Analytics initiatives that are distinct in domains and can guide future research collaboration and focus. The research was conducted on the example of Logistics and Supply Chain Management and the respective domain-specific Analytics subfield of Supply Chain Analytics. The field of Logistics and Supply Chain Management has been recognized as early adopter of Analytics but has retracted to a midfield position comparing different domains. Design/methodology/approach: This research uses Grounded Theory based on 12 semi-structured Interviews creating a map of domain characteristics based of the paradigm scheme of Strauss and Corbin. Findings: A total of 34 characteristics of Analytics initiatives that distinguish domains in the execution of initiatives were identified, which are mapped and explained. As a blueprint for further research, the domain-specifics of Logistics and Supply Chain Management are presented and discussed. Originality/value: The results of this research stimulates cross domain research on Analytics issues and prompt research on the identified characteristics with broader understanding of the impact on Analytics initiatives. The also describe the status-quo of Analytics. Further, results help managers control the environment of initiatives and design more successful initiatives.DFG, 414044773, Open Access Publizieren 2019 - 2020 / Technische Universität Berli