scholarly journals On the Periodic Gain of the Ribosome Flow Model

2018 ◽  
Author(s):  
Mahdiar Sadeghi ◽  
Muhammad Ali Al-Radhawi ◽  
Michael Margaliot ◽  
Eduardo Sontag
Keyword(s):  
Production Rate ◽  
Compartmental Model ◽  
Flow Model ◽  
Point Of View ◽  
Periodic Pattern ◽  
Rigorous Analysis ◽  
Instantaneous Rate ◽  
Rna Translation ◽  
Average Production ◽  
Relevant Quantity

We consider a compartmental model for ribosome flow during RNA translation called the RFM. This model includes a set of positive transition rates that control the flow from every site to the consecutive site. It has been shown that when these rates are time-varying and jointly T-periodic every solution of the RFM converges to a unique periodic solution with period T. In other words, the RFM entrains to the periodic excitation. In particular, the protein production rate converges to a unique T-periodic pattern. From a biological point of view, one may argue that the average of the periodic production rate, and not the instantaneous rate, is the relevant quantity. Here, we study a problem that can be roughly stated as: can periodic rates yield a higher average production rate than constant rates? We rigorously formulate this question and show via simulations, and rigorous analysis in one simple case, that the answer is no.

scholarly journals Maximizing protein translation rate in the non-homogeneous ribosome flow model: a convex optimization approach

2014 ◽  
Vol 11 (100) ◽  
pp. 20140713 ◽  
Author(s):  
Gilad Poker ◽  
Yoram Zarai ◽  
Michael Margaliot ◽  
Tamir Tuller
Keyword(s):  
Synthetic Biology ◽  
Convex Optimization ◽  
Production Rate ◽  
Protein Production ◽  
Flow Model ◽  
Protein Translation ◽  
Optimization Approach ◽  
Initiation Rate ◽  
Translation Rate ◽  
Protein Production Rate

Translation is an important stage in gene expression. During this stage, macro-molecules called ribosomes travel along the mRNA strand linking amino acids together in a specific order to create a functioning protein. An important question, related to many biomedical disciplines, is how to maximize protein production. Indeed, translation is known to be one of the most energy-consuming processes in the cell, and it is natural to assume that evolution shaped this process so that it maximizes the protein production rate. If this is indeed so then one can estimate various parameters of the translation machinery by solving an appropriate mathematical optimization problem. The same problem also arises in the context of synthetic biology, namely, re-engineer heterologous genes in order to maximize their translation rate in a host organism. We consider the problem of maximizing the protein production rate using a computational model for translation–elongation called the ribosome flow model (RFM). This model describes the flow of the ribosomes along an mRNA chain of length n using a set of n first-order nonlinear ordinary differential equations. It also includes n + 1 positive parameters: the ribosomal initiation rate into the mRNA chain, and n elongation rates along the chain sites. We show that the steady-state translation rate in the RFM is a strictly concave function of its parameters. This means that the problem of maximizing the translation rate under a suitable constraint always admits a unique solution, and that this solution can be determined using highly efficient algorithms for solving convex optimization problems even for large values of n . Furthermore, our analysis shows that the optimal translation rate can be computed based only on the optimal initiation rate and the elongation rate of the codons near the beginning of the ORF. We discuss some applications of the theoretical results to synthetic biology, molecular evolution, and functional genomics.

scholarly journals Ribosome flow model with extended objects

2017 ◽  
Vol 14 (135) ◽  
pp. 20170128 ◽  
Author(s):  
Yoram Zarai ◽  
Michael Margaliot ◽  
Tamir Tuller
Keyword(s):  
Steady State ◽  
Production Rate ◽  
Protein Production ◽  
Flow Model ◽  
Mean Field ◽  
State Density ◽  
Transition Rates ◽  
Ribosome Density ◽  
Protein Production Rate ◽  
Unique Steady State

We study a deterministic mechanistic model for the flow of ribosomes along the mRNA molecule, called the ribosome flow model with extended objects  (RFMEO). This model encapsulates many realistic features of translation including non-homogeneous transition rates along mRNA, the fact that every ribosome covers several codons, and the fact that ribosomes cannot overtake one another. The RFMEO is a mean-field approximation of an important model from statistical mechanics called the totally asymmetric simple exclusion process with extended objects (TASEPEO). We demonstrate that the RFMEO describes biophysical aspects of translation better than previous mean-field approximations, and that its predictions correlate well with those of TASEPEO. However, unlike TASEPEO, the RFMEO is amenable to rigorous analysis using tools from systems and control theory. We show that the ribosome density profile along the mRNA in the RFMEO converges to a unique steady-state density that depends on the length of the mRNA, the transition rates along it, and the number of codons covered by every ribosome, but not on the initial density of ribosomes along the mRNA. In particular, the protein production rate also converges to a unique steady state. Furthermore, if the transition rates along the mRNA are periodic with a common period  T then the ribosome density along the mRNA and the protein production rate converge to a unique periodic pattern with period  T , that is, the model entrains to periodic excitations in the transition rates. Analysis and simulations of the RFMEO demonstrate several counterintuitive results. For example, increasing the ribosome footprint may sometimes lead to an increase in the production rate. Also, for large values of the footprint the steady-state density along the mRNA may be quite complex (e.g. with quasi-periodic patterns) even for relatively simple (and non-periodic) transition rates along the mRNA. This implies that inferring the transition rates from the ribosome density may be non-trivial. We believe that the RFMEO could be useful for modelling, understanding and re-engineering translation as well as other important biological processes.

New Steps to Improve Rotordynamic Stability Predictions of Centrifugal Compressors

2008 ◽  
Vol 130 (2) ◽  
Author(s):  
Manoj K. Gupta ◽  
Thomas A. Soulas ◽  
Dara W. Childs
Keyword(s):  
Centrifugal Compressor ◽  
Flow Model ◽  
Aerodynamic Performance ◽  
Magnetic Bearing ◽  
Point Of View ◽  
Test Results ◽  
Performance Point ◽  
Pressure Test ◽  
Full Pressure ◽  
Rotor Model

Improved rotordynamic stability is desired by end users, and centrifugal compressor manufacturers are expected to meet, if not exceed, this expectation. Compressor manufacturers are required to design and build machines that are rotordynamically stable on the test stand and in the field. Confidence has been established in predicting the excitation forces from seals and bearings, but impeller aerodynamic excitation forces continue to be a challenge. While much attention is paid to impellers from an aerodynamic performance point of view, more efforts are needed from a rotordynamic standpoint. A high-pressure, reinjection centrifugal compressor is analyzed in order to predict rotordynamic stability using the best available resources for seals and bearings. Impeller shroud forces are predicted using the bulk-flow model developed by Gupta and Childs (Gupta, M., and Childs, D., Proc. of ASME Turbo Expo 2000, Power for Land, Sea, and Air). Each impeller stage is analyzed and an attempt is made to improve the estimation of impeller aerodynamic excitation forces. Logarithmic decrement (log dec) predictions for the full rotor model consisting of all the stages and seals are compared to the full-load full-pressure test measured values using a magnetic bearing exciter. A good correlation is obtained between the measured test results and analytical predictions.

Cosmic Ray Positron Production by Gamma Ray Interactions on Starlight

1991 ◽  
Vol 9 (1) ◽  
pp. 115-117 ◽  
Author(s):  
A. Mastichiadis ◽  
R. J. Protheroe ◽  
S. A. Stephens
Keyword(s):  
Production Rate ◽  
Unit Volume ◽  
Gamma Ray ◽  
Cosmic Ray ◽  
High Energy ◽  
Local Region ◽  
Positron Energy ◽  
Average Production ◽  
The Galaxy ◽  
Positron Production

AbstractWe examine the production of cosmic ray positrons by photon-photon pair production of high-energy γ-rays on starlight photons. We start by calculating the production rate as a function of positron energy and distance from the Sun resulting from interactions with sunlight. The results are generalized to production on other types of star. We calculate the average production rate per unit volume averaged over the local region of the galaxy, and we estimate the contribution to the observed intensity from this process.

scholarly journals ANALISIS POLA MIGRASI DAN KONSUMSI RUMAH TANGGA DI DESA PESISIR TERKAIT KEMISKINAN DAN KERENTANAN PANGAN

2017 ◽  
Vol 4 (2) ◽  
pp. 185
Author(s):  
Armen Zulham ◽  
Subhechanis Saptanto ◽  
Retno E. Rahmawati ◽  
Lindawati Lindawati ◽  
Teuku Fauzi
Keyword(s):  
Corporate Social Responsibility ◽  
Social Responsibility ◽  
Positive Impact ◽  
Point Of View ◽  
Survey Method ◽  
Periodic Pattern ◽  
Consumption Pattern ◽  
Economic Point ◽  
Client Relationship ◽  
Corporate Social

Penelitian ini bertujuan untuk mempelajari pola migrasi masyarakat pesisir, mengidentifikasi determinan migrasi, mengkaji keterkaitan antara arus tenaga kerja, uang, barang dan jasa karena migrasi. Penelitian dilakukan pada bulan September-Oktober 2009 dengan menggunakan metode survey pada migran di daerah asal dan daerah tujuan migrasi. Responden yang dipilih adalah migran berdasarkan daerah asal dan daerah tujuan migrasi berjumlah 45 responden. Hasil penelitian ini menunjukkan bahwa migrasi dari daerah pesisir didorong oleh kelangkaan potensi ikan di perairan pesisir dan terbatasnya akses masyarakat terhadap perekonomian desa serta tersedianya pekerjaan di daerah tujuan migrasi. Keputusan bermigrasi karena jaminan pekerjaan. Pola migrasi umumnya adalah migrasi sirkulasi: mingguan dan bulanan. Migrasi itu mendorong terjadinya aliran tenaga kerja, uang dan barang antara daerah asal migrasi dan daerah tujuan migrasi. Secara ekonomi migrasi tersebut memberi dampak positif terhadap pertumbuhan perekonomian di desa asal migran dan daerah tujuan migran. Rata-rata jumlah yang bermigrasi per keluarga adalah sekitar 2 orang dan jumlah uang yang dikirim karena migrasi ke desa asal migran mencapai Rp. 500 juta per bulan. Migrasi cenderung mendorong terjadinya pengelompokanmasyarakat menurut pekerjaan dan tempat tinggal di daerah tujuan migrasi, karena adanya hubungan “patron client” antara pemilik modal (patron) dan migran (client). Migrasi merupakan salah satu alternatif masyarakat pesisir untuk keluar dari masalah kemiskinan dan memenuhi kebutuhan pangan rumah tangganya. Hasil penelitian ini merekomendasikan agar program-program bantuan termasuk corporate social responsibility (CSR) yang masuk ke desa pesisir harus dikonsolidasikan dengan modal/aset yang dihimpun oleh para migran untuk menjadi pengungkit perekonomian desa pesisir. Tittle: Analysis of Migration and Household Consumption Pattern in the Coastal Villages Related to Poverty and Food Resiliency.The purpose of this research was to study the migration pattern, to identify the determinant of migration, to investigate the dependency between labor movement, money, good and services. The data were collected in September 2009 and October 2009 by using survey method. Respondents were migrant based on migrant origin and migrant destination accounted for as 45 person. Results of the study showed as the following: migration from coastal villages where due to the depletion of fish in coastal water, limited access in local economic gain, and the availability of occupation in labor destination places. Weekly and monthly migration (periodic) pattern are common in both migrant destination and origin areas. Migration persuades the movement of labor, money, good and services between labor destination and origin places. From economic point of view, migration gives a positive impact to migrant destination and origin areas, respectively. In an average, 2 labors in each household in coastal villages were migrant, and Rp. 500 million were transfer to each respective village. Migration tends to push establishing society group according to type of recepation and residential place in the migration destination due to patron client relationship. Migration for the coastal community seems, to be one alternative to alleviate poverty and provide food for household. Results of the research recommend that aid’s programs including the corporate social responsibility (CSR) in coastal village should be consolidated with the accumulate asset of the migrant in stimulating economic development of their respective village.

Producing mice for bioassays

1980 ◽  
Vol 14 (3) ◽  
pp. 229-232
Author(s):  
Margaret Ryle
Keyword(s):  
Production Rate ◽  
Experimental Animals ◽  
Pregnant Females ◽  
Foster Mothers ◽  
Average Production

Groups of breeding females were caged together for 3 weeks before putting them (1 or 2 per small box) with males, for 4-5 days. They were then pooled again until shortly before parturition. The majority of pups were born 22 or 23 days after pairing and were reared in foster litters, usually consisting of 27 pups with 3 foster mothers. Non-pregnant females and those not required as foster mothers were pooled once more. All pups were weaned on the same day, 19 or 20 days after birth, when all females were again mated. The average production rate was approximately 4 usable pups per female in the batch every 6 weeks. By maintaining 3 asynchronous batches of females a regular fortnightly supply of experimental animals was maintained with minimum wastage of food and labour.

The global-average production rate of10Be

1986 ◽  
Vol 76 (3-4) ◽  
pp. 279-287 ◽  
Author(s):  
Marc C. Monaghan ◽  
S. Krishnaswami ◽  
Karl K. Turekian
Keyword(s):  
Production Rate ◽  
Global Average ◽  
Average Production

Modelling Study to Evaluate Two Variants for Accessing a Deep Geological Repository From the Point of View of Long-Term Safety

2013 ◽  
Author(s):  
Andreas Poller ◽  
Paul Smith ◽  
Gerhard Mayer ◽  
Mohamed Hayek ◽  
Jürg W. Schneider ◽  
...  
Keyword(s):  
Network Flow ◽  
Flow Model ◽  
Transport Model ◽  
Point Of View ◽  
Access Route ◽  
Deep Geological Repository ◽  
Acceptable Solution ◽  
Geological Repository ◽  
Exact Position

Siting a deep geological repository for radioactive waste essentially involves two interrelated steps: deciding on an appropriate geological environment for the underground facilities and selecting a suitable location for the associated surface facility. An acceptable solution is more easily achieved if some flexibility exists for siting the surface facility, irrespective of the exact position of the underground facilities. Such flexibility is available if a ramp is used as the main access route from the surface facility to the underground facilities. Another option is to use a combination of shafts and (sub)horizontal tunnels as the main access route. Both variants include shafts for ventilation, etc. In this paper, the two variants (i) main access via ramp and (ii) main access via shaft are compared in terms of long-term safety. To this end, the entire network of underground tunnels of a deep geological repository is implemented in an analytical resistor network flow model. Radionuclide release through the tunnel system and the host rock is then calculated with a numerical network transport model, using as input the results from the flow model. The results clearly indicate that, even in case of hypothetically deficient horizontal and subhorizontal sealing elements, the choice between ramp and shaft as the main access route is irrelevant to long-term safety.

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